How to Run Payroll, a Step-by-Step Guide

How to Run Payroll, a Step-by-Step Guide

Ready to run payroll in BerniePortal? Follow along with this step-by-step guide. Before you begin, check out these tips and suggestions.

  1. Configure your employer’s pay dates.
  2. Ensure all employees are in a Payroll subgroup. 
  3. Approve all outstanding Time and PTO requests for the pay period. 
    1. You can edit an employee’s Time and PTO while running payroll, if necessary.
  4. Process any terminations that may impact the pay period for which you intend to run payroll.
    1. You can exclude employees while running payroll, if necessary. 
  5. Encourage employees to complete any outstanding enrollments that may impact the pay period for which you intend to run payroll.
    1. You can edit an employee’s deductions while running payroll, if necessary.
  6. Set up any Custom Earning and Deduction Types you may need. 
  7. Ensure employees have completed standard Direct Deposit, W4, and State Withholding (if applicable) onboarding documents.

To run payroll:
  1. Select the “Payroll” tab in the top navigation menu. 
  2. Select the “Run Payroll” tab in the secondary navigation menu. 
  3. Use the “Subgroup” dropdown menu to select the Payroll subgroup for which you’d like to run payroll.
  4. Use the “Pay Period” dropdown menu to select the pay period for which you’d like to run payroll. (Note: Payroll must be run at least three banking days in advance in order to be paid on the displayed pay date unless you've been authorized for two day processing).
  5. Select “Open Payroll.”

  7. Note: If at any point after opening payroll, you need to pause and resume payroll at a later time, all changes are saved as you progress. Learn how to resume an open payroll here.
  8. If any employees are missing crucial information, an error message will display in red at the top of the table.
    1. Employees who are missing crucial information are unable to be included with the payroll run, and will display in a disabled state. 
    2. If an employee is missing information such as their SSN, the information must be entered in their profile, and the payroll run must be re-opened in order to include the employee in the payroll run. To do so, scroll to the bottom of the screen and select “Start Over.”
  9. If Benefit Deductions aren’t required for the pay period, select “Skip benefit deductions for this pay period.” The Benefit Deductions column will be hidden, and all employee benefit deductions will be excluded from the payroll run. 

  11. Employees are listed alphabetically by their last name. Take a moment to ensure all employees that should be included are listed and selected. If any employees should be excluded from the payroll run, use the checkbox beside their name to deselect them.
  12. Compensation:
    1. Exempt employees are listed with their per pay period compensation. 
    2. Non-exempt employees are listed with their hourly rate.
    3. Employees with missing compensation information in BerniePortal will default to $0.00. Please review the yellow warnings area for a list of employees with a $0.00 compensation, and make changes if necessary. 
    4. If you need to make changes to an employee’s compensation, make the change directly in the employee’s compensation field. Note that this does not update the employee’s compensation in BerniePortal. Changes are reflected for the payroll run only. 
  13. Overtime Rate (OT Rate):
    1. Exempt employees will not display an Overtime Rate. 
    2. Non-exempt employees will display their Hourly Overtime Rate (Rate per Hour * Overtime Factor).
    3. Employees with missing Overtime Factor information in BerniePortal will default to $0.00. Please review the yellow warnings area for a list of employees with a $0.00 Overtime Rate, and make changes if necessary. 
    4. If you need to make changes to an employee’s OT Rate, make the change directly in the employee’s OT Rate field. Note that this does not update the employee’s profile or timesheet in BerniePortal. Changes are reflected for the payroll run only. 
  14. Hours (HRS):
    1. Exempt employees will not display hours. 
    2. Non-exempt employees will display the total number of hours they’ve logged in BerniePortal’s “Time and Attendance” feature for the applicable pay period. 
    3. If you need to make changes to an employee’s hours, make the change directly in the employee’s hours field. Note that this does not update the employee’s timesheet in BerniePortal. Changes are reflected for the payroll run only. 
  15. Overtime Hours (OT Hours):
    1. Exempt employees will not display Overtime Hours. 
    2. Non-exempt employees will display the total number of overtime hours they’ve logged in BerniePortal’s “Time and Attendance” feature for the applicable pay period, based on their Time & Attendance subgroup’s overtime rules. 
    3. If you need to make changes to an employee’s overtime hours, make the change directly in the employee’s overtime hours field. Note that this does not update the employee’s timesheet in BerniePortal. Changes are reflected for the payroll run only. 
  16. PTO (Paid Time Off Hours):
    1. Exempt employees will not display PTO Hours. Holiday hours are included per the employee’s PTO subgroup’s Holiday rules. 
    2. Non-exempt employees will display the total number of PTO hours they’ve logged in BerniePortal’s “PTO” feature for the applicable pay period, and Holiday hours are automatically included per the employee’s PTO subgroup’s Holiday rules. 
    3. If you need to make changes to an employee’s PTO hours, make the change directly in the employee’s PTO field. Note that this does not update the employee’s PTO history or timesheet in BerniePortal. Changes are reflected for the payroll run only. 
  17. Earnings:
    1. Review employee “Earnings” by selecting the bubble beside that employee’s Earnings total. 
    2. Available Earning types will be listed. Type a value in the desired input field to add Earning amounts. 

    4. Select the “Recurring” checkbox beside an Earning type to repeat that Earning Type and Amount each pay period. 
    5. Select “I’m Done.”
  18. Reimbursements:
    1. Enter an employee's Reimbursement total in their "Reimbursements" field.
  19. Deductions:
    1. Review employee “Deductions” by selecting the bubble beside that employee’s Deductions total. 
    2. Available Deduction types will be listed. Type a value in the desired input field to add Deduction amounts. 

    4. Select the “Recurring” checkbox beside a Deduction type to repeat that Deduction Type and Amount each pay period. 
    5. Select “I’m Done.”
  20. Benefit Deductions:
    1. Review a breakdown of employee “Benefit Deductions” by selecting the bubble beside that employee’s Benefit Deductions total. 
    2. If adjustments are needed, make the change by benefit type or bucket, then select “I’m Done.” 

    4. Note that this does not update the employee’s Benefit Enrollment in BerniePortal. Changes are reflected for the payroll run only.  
  21. Gross Total:
    1. An employee’s Gross Total consists of their Compensation, Overtime Pay, PTO Pay, and Earnings. 
  22. Total Payroll:
    1. A payroll run’s Total Payroll is the sum of all included employee’s Gross Totals.
  23. Ensure all employee information is correct, all Errors and Warnings have been resolved, and you’ve reviewed the listing of employees to ensure the appropriate employees are included/excluded, then select “Save & Review.”
    1. If you’d like a clean slate for the selected pay period, select “Start Over.” All progress will be cleared, and you can re-open a new payroll run for the applicable pay period. 
  24. Review payroll run totals, as well as employee and employer tax information by selecting the appropriate bubble icons. If you’d like to make further changes, select “Back to Edit.” Otherwise, select “Run Payroll” to begin processing the payroll run. 
  25. Selecting “Run Payroll” navigates you to the “History” area, where you can review submitted payroll information, and check the status of submitted payroll runs. Learn more about the History tab here.


Note: Need to run an off-cycle payroll run, for example, bonuses? Contact us at help@bernardhealth.com.

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