Run Payroll

Purpose: This help guide will walk you through the three steps of processing your payroll. 

Did you know we have a BambooHR Learning course about running payroll? Click here to learn more about what is included in this course.

Which employee data is in the payroll?

Please note that starting the payroll process will take a snapshot of the employee data as of the pay cycle start date. Therefore, you will want to make any essential changes or additions to your employees before running payroll. If you have an employee data change that is effective during the pay cycle, it will not automatically include in the current payroll. Instead, those changes will be effective in the payroll following the effective date. If you need to have the change included in the current payroll, you will need to override the changes during Step 2 of payroll manually or hit Update next to the applicable employee in Step 1 (see Step 1 below).

Employees will only be in the payroll run if they have active records as of the pay cycle start date.

  1. If an employee has a wage or demographic record end and a new record starts within the pay period range, we will use the record that was effective at the beginning of the pay period for reference on which information to use on the payroll. This may cause an employee to be underpaid. If you need to override this, you can do so in Step 2 of running payroll. 
  2. If an employee is terminated during a pay cycle but was active on the pay cycle start date, we will still include them in that payroll run. Please complete the Final Pay Date field during offboarding to prevent missing pay for a terminated employee.
  3. We will check for any new hire dates that fall within the current pay cycle to ensure new hires are not excluded from payroll if they start in the middle of a pay cycle. New hires must also have active wage and demographic effective dates to be in the current payroll.  

Run payroll in the Payroll Center

All payroll runs are processed in the Payroll Center using an easy, three-step process. To get started, go to the Run Payroll tab found in the Payroll Center. You will see a list of available payrolls with specifics about each payroll, including the payroll start and end dates.

1. Run Payroll: If you have not started the payroll, you can click Run Payroll to begin your payroll run.  Be sure to verify that your pay dates are accurate first. 

If you have already started working on your payroll, you will see options to click Continue Payroll or Reset Payroll instead.  

2. Continue Payroll: Choosing Continue Payroll will bring you back to the payroll data you were working on previously. The system will automatically sync when you click Continue Payroll to make sure there are no new deductions on the company or employee level. If there are, they will apply to the employee's record. If any errors related to the sync occur, you will see an error message at the top of the screen requiring you to fix the deduction error before continuing the payroll. 

3. Reset Payroll: If you have started a payroll run but have determined that you need to make changes or start over, click the Reset Payroll button to refresh and restart your current payroll run. A pop-up box will appear asking you to confirm that you understand that this will be resetting your payroll run, and you will have to re-enter all changes, including hours worked. Clicking OK will immediately trigger the running of auto-sync and then re-open the payroll.

Clicking on any one of the three options (Run Payroll, Continue Payroll, or Reset Payroll) will bring you to a new screen where you will follow through with the three steps of processing payroll.

Run payroll

  1. Payroll parameters: At the top of the new screen, you will see the payroll parameters listed, including the Payroll Type, Pay Date, Pay Period Start Date, Pay Period End Date, Due Date, and the unique Pay Cycle ID number. 
  2. Search Section: There are search fields available to make it easier to search for specific employees within this payroll cycle. You can search by Wage Type, Department Type, and Tax Type.
  3. Search box: You can also use the Search box to search for an employee by name or other qualifying factors.
Step 1 - Review and update hours and time off
What options are available for adding hours to TRAXPayroll?

As you read through getting hours in Step 1 of Running Payroll, you will learn about two options for getting your employees' work hours into TRAXPayroll. Here is a summary of each option and how it works:

  1. BambooHR Time Tracking: If you use BambooHR Time Tracking, you will see a Get Hours button in Step 1 of Run Payroll. This will automatically pull any approved hours worked during the pay period for the employees included in the payroll run.
  2. Third-Party time tracking solution: If you use another system to track hours worked, you will need to import those hours into BambooHR using the hours importer. Once you have imported the hours into BambooHR, you will follow one of the steps above depending on if you use Remote Link or Autosync.

Within the first-step screen, there are several features available that will help speed up the payroll management process.

  1. Zero All Wages: By clicking Zero All Wages, you will zero out all regular wages for a specific payout event such as a bonus or commission payroll run. However, this will not zero additional wage types of which you can clear using the Global Payroll Update Button in Step 2.
  2. Get Hours: If you use BambooHR Time Tracking, clicking Get Hours will pull Time Off, Holiday,* and Time Tracking hours, if applicable, from BambooHR. Double Time hours will populate in the Other Hours category. *Note: You can edit the value pulled over into the Holiday column. If you do not use BambooHR Time Tracking, you will need to import your hours in BambooHR to add them to payroll. The Get Hours button will pull those imported hours from BambooHR into your payroll run.
  3. Add Employee: Click Add Employee to include an employee in this payroll who you usually do not include or no longer include in payroll. Please note that employees who do not have active wage and demographic records will not show up in the list.  Every time you click this button, the system will sync a refreshed list of available employees to the pay schedule in order to add them to the payroll. You can only pull employees assigned to the corresponding pay group into the payroll run. If an error related to the employee sync occurs, you will see an error message at the top of the screen telling you to fix the employee errors before adding them to the payroll.

4. Update: Clicking Update will refresh the applicable employee's sync from BambooHR when you need to re-sync the employee's information in the payroll run. If an error related to the employee sync occurs, you will see an error message at the top of the screen telling you to fix the employee errors before updating their information in payroll.

5. Delete: Clicking Delete enables you to remove an employee from the payroll if needed.

6. Clear All: Click Clear All if you would like to uncheck all employees, and then you can check the box next to each specific employee you need for the payroll run.

7. Review and Make Edits: You can review and make edits to any of the fields in the payroll cycle except those that are grayed-out. If an employee has grayed-out fields, they do not have a wage rate for that hour type, or that time off type is not available on their employee record.

8. Preview Hours Input Sheet: You have the option to preview your hours entered before moving to the next step by clicking on Preview Hours Input Sheet. Note: Make sure you click Save before choosing to preview, or the data will not be on the report. 

9. Save Changes: If you have made revisions, click Save Changes to make sure you have saved the revisions before navigating away from this page.

10. Next: Clicking Next will save your changes and take you to Step 2.

Step 2 - Review and update additional pay

Step 2 of your payroll run allows you to review and enter any additional pay. If needed, it also allows you to change federal withholding elections to a flat percentage for special circumstances, such as a bonus payout. You can add extra pay during this step and one-time overrides. 

  1. Search Section: You can double-click on Search Section to expand the section to include Wage Type, Department Type, and Tax Type. 
  2. Global Payroll Update: You can make changes to specific items for all employees in the entire payroll run. Keep in mind that these changes are only for the current payroll; they will not affect the employee's permanent record. To get started making changes to the entire payroll run, click Global Payroll Update. In the Global Payment Update pop-up, you will have several options available. 
Want to learn more about global payroll updates?
  • Return to Step 2: At any point, you can choose Return to Step 2 without making any global updates. 
  • Additional Pay Expense Section: If employees have recurring pay on their wage records, such as expense reimbursements, you can remove those for the payroll run by clicking Update All Additional Pay.
  • Employee Bank Section: You can choose to issue paper checks for all employees by clicking the Yes radio button and then clicking Update All Printable Checks.
  • Tax Section: You can change the tax frequency of the payroll run from the normal pay period taxing schedule. From the drop-down list, choose Annually, Bi-weekly, Daily, Monthly, Quarterly, Semi-annually, Semi-monthly, or Weekly. This is very useful during a bonus run. After you select the tax frequency, click Update All Frequencies to save your changes. You can also set federal income tax to a flat percentage for all employees,  such as 22% for the supplemental pay rate. Once you have typed the percentage number, click Update All Fed WH to save your changes.
  • Deduction/Accrual/Garnishment Section: You can suppress deductions, garnishments, and hour benefits by choosing the Yes radio option next to the appropriate item. Keep in mind that suppressing benefits will prevent manual debits and credits from posting during this payroll cycle. Be sure to click Update Suppressions after making your selection.
  • Close: Once you have made all the needed changes, click Close to return to Step 2. 

3. Search: You can also use the Search box to search for an employee by name or other qualifying factors.

4. Delete: Clicking Delete enables you to remove an employee from the payroll if needed. 

5. Edit: You can make one-time override adjustments on each employee. Click Edit next to the employee's name to go to the Edit Step 2 screen for the individual employee. Here, you can add extra payments, make one-time changes to update withholding elections, tax frequencies, deductions, etc. Changes made under Edit will only affect the current payroll run. 

Want to learn more about one-time override adjustments?
  • Wage & Extra Pay Section: In these sections, the employee's wage information will show, including Wage Type, Overtime Status, Salary, Other Rate, and Overtime Rate. Also, you can add up to three extra pay types for an employee. Enter the amount of extra pay and select the pay type from the drop-down menu.
  • Timesheet Hours & Additional Information: Entered Regular Hours, Other Hours, and Overtime Hours will show in the Time Sheet Hours section. You can also enter notes under Additional Information. These notes will add to the employee's pay stub.
  • Federal Withholding & State Withholding & State Unemployment Insurance & Tax Sections: There are four sections where you can change an employee's tax elections and amounts for the current payroll run. Also, you can change the tax frequency of the payroll to affect taxing if necessary.
  • Employee Bank Section: This allows changes in employee payment options for the current payroll run. If the employee has multiple banks, you can choose to send the money to only one account or override the banking information for a printable check. When you select Send money to one account? the system will automatically sync current bank information. If any errors occur during the bank information sync, you will see the associated error message at the top of the screen. You will need to resolve the errors before you can select the corresponding bank for payment.
  • Deduction/Accrual/Garnishment Section: Enter any one-time adjustments during payroll to correct employee deductions and garnishments. 
  • Override Amounts: Enter override amounts here. Enter the amount to be adjusted that includes the current payroll deduction. This amount will deduct in the payroll run instead of the usual deduction amount. If a deduction has been over-collected, enter a negative amount in the Employee Override Amount field.
  • Employer Override Amount: Enter override amounts here. Enter the amount to be adjusted that includes the current payroll deduction. This amount will deduct in the payroll run instead of the usual deduction amount. If a deduction has been over-collected, enter a negative amount in the Employer Override Amount field.
  • Please note that it is not allowed to reverse collectible deductions such as garnishments.
  • Additional Pay Expense Section: You can delete or suppress additional pay and expenses in this section by clicking Delete or checking the Suppress box respectively.
  • Make sure to click Save at the top of the page so your revisions will be made to the current payroll run, or click Cancel at any time to exit this section and return to Step 2 in the Payroll Center.

6. Add Check: Click Add Check to add additional checks for employees. This will add separate paychecks so that they can be taxed differently. 

7. Review and Make Edits to Extra Pay Amounts and Pay Types: To add extra pay types to an employee, enter the amount in the Extra Pay 1 column and select the pay type from the drop-down list. Remember, if you click Edit, you can add two more extra pay amounts and types if needed. However, make sure that you save the information entered before clicking Edit

8. Preview Additional Pay/Expense: A report of additional pay entries is available to review by clicking Preview Additional Pay/Expense. Be sure to click Save Changes before choosing to preview the report. 

9. Back: Select Back if you need to return to Step 1 for any reason, but remember to save your changes.

10. Save Changes: Changes do not save automatically, so remember to click Save Changes before navigating to any other screens. 

11. Calculate Payroll: Once you have entered any additional pay and have made any necessary changes, click Calculate Payroll to move on to Step 3 and finalize your payroll run.

Virginia's Overtime Requirements

Please be sure to refer to Virginia's state tax website for overtime wage rules. 

Currently, TRAXPayroll does not calculate this. 

Since the calculations are required by a 40-hour workweek, you could opt for biweekly or weekly pay frequencies for hourly employees (workweek may be determined by a company i.e. Monday - Sunday or Sunday - Saturday, etc) as this will allow programming calculations a bit easier. 

Once you have determined the dollar amount, you will need to add as an additional pay type in step 2 of Run Payroll using the option "Additional Overtime Pay". (see above) These calculations are applicable according to your own company guidelines and tax laws.

The system will automatically sync certain information when you click Calculate Payroll to move on to Step 3. The following information will sync:

  1. Employee Deduction and Company Deduction: This sync will calculate the deduction amount, cap amount, and global limit.
  2. Employee Termination Date: To calculate hours on salary employees, we check employee termination dates. This will sync all employees in the pay schedule to ensure that all termination date information in BambooHR is up to date in TRAXPayroll.
  3. Direct Deposit Information: This will sync the employee bank information. This ensures we have the most up-to-date bank information for all employees included in the payroll.

If any errors occur during any of the syncs listed above between Step 2 and Step 3, you will remain on Step 2 of payroll to resolve all errors listed. You will not be able to move on to Step 3 until you resolve the errors.

Step 3 - Review and approve payroll

In Step 3, you can review the payroll data for accuracy before approving it.

  1. Review Each Employee: This shows a list of each employee with their wages, taxes, deductions, and net pay. You can easily click on an employee's name to view a PDF of their unapproved earnings statement (pay stub). This makes it easy to review each pay stub for accuracy before finalizing payroll. 
  2. Deposit Limit: If a single direct deposit is over $100,000, our bank (NPC) will require submission of the entire amount for the payroll to be via wire. You can see this employee's pay information is highlighted in red for you to be aware of the limit. Please contact our customer support team to arrange wiring the funds for the entire payroll.
  3. Total to be electronically transmitted: The amount of the payroll debit includes direct deposits, employee and employer taxes, collectible garnishments (if any), and fees. Garnishments for tax levies (child support, etc.) can be set up to be collected and paid by TRAXPayroll. They are considered collectible deductions and are in the payroll debit for us to pay them on your behalf. Uncollected deductions, such as health insurance, dental insurance, are not in the debit. They stay in your bank account for you to distribute as needed. Checks to Print will also not show up under the total debit but will show under the Total Cash Requirement needed to process this payroll. 
  4. Reports: A variety of reports are available to help you review your payroll for accuracy before approving the payroll. All entered data will be preserved. 
  5. Cancel: If you need to make changes, you can click Cancel. This will take you back to the Payroll Center, where you can choose to continue the payroll again and make changes as needed. If you want to cancel the payroll, all data will remain intact so that you can make the necessary changes without losing what you have already entered.
  6. Approve Pay Date: Once you have confirmed that all information is correct, click Approve Pay Date to finalize your payroll. Once payroll is approved, the payroll's status will show as Pending until processed on the due date. You can approve payrolls in advance of the due date, and they will not process until the due date. The pay date is on the Approve button for easy reference. On the Approve Payroll Process page, you can view your pay cycle details and View Pay Cycle reports. (See below.)

The system will sync all hour benefits and accruals in BambooHR to ensure the use of all correct information when we upload the final payroll and generate paystubs. If an error occurs with this sync, you will need to resolve it before approving the payroll.

Confirmation email

Confirmation email: A confirmation email will send to the approver. Other admins can receive the approval email also if marked as such in the Company Users tab. A second confirmation email will send to the approver after the processing of payroll by TRAXPayroll.

How do I reopen a payroll run to make changes?

If you need to reopen a submitted payroll to make changes, you will see a Reopen Payroll button on pending payrolls that will be available until 12 PM Pacific Time on the due date. 

Click Reopen Payroll, and you will see a confirmation pop-up box to confirm your action.

Once confirmed, you can click Continue Payroll to make the necessary changes.

If you need to make a change to a locked payroll run, you can contact our support team to reopen the payroll. If you have multiple payrolls in your payroll center, please be specific about which one you want to reopen. The Pay Cycle ID is the best way to identify a specific payroll. You can find this six-digit number in the payroll center next to Waiting for funds to transfer. Please note that there is no guarantee it can be reopened if the files have already been sent to the bank, but there is a $10 fee for successfully reopening a locked payroll.

What's next?

Did you miss the payroll processing deadline?

Do you have more questions about payroll?

Would you like to use the sample tax calculator?