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

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

Ready to process payroll in BerniePortal? Follow this comprehensive guide to ensure accurate and timely payroll runs. Before beginning, review our preparation tips and timing requirements.

Important Timing Requirement: 
  1. Submission deadline: Submit payroll by 2:00 PM local time, at least 2 days before the check date to allow for processing
  2. Contact your Account Manager directly if you are unable to meet this deadline at any time


Payroll Preparation
  1. Configure the customizable check dates
  2. Ensure all employees are in an appropriate Payroll subgroup
  3. Approve all outstanding Time and PTO requests for the pay period
    1. Employee’s Time and PTO information can be altered while running payroll, if necessary
  4. Process any terminations that may impact the upcoming pay period
    1. Employees can be excluded while running payroll, if necessary
  5. Encourage employees to complete any outstanding enrollments that may impact the upcoming pay period
    1. Employee deductions can be adjusted while running payroll, if necessary
  6. Ensure that any needed custom Earning and Deduction codes have been added by your Account Manager
  7. Ensure employees have completed standard Direct Deposit, W4, and State Withholding (if applicable) onboarding documents


Run Payroll

To access: 
  1. Log in to BerniePortal as the Global Administrator or a Payroll Feature Admin
  2. Select “Payroll” in the top navigation menu
  3. Select “Run Payroll” in the secondary navigation window
  4. Use the “Subgroup” dropdown menu to select the Payroll subgroup for which payroll needs to be processed
  5. Use the “Pay Period” dropdown menu to select the appropriate pay period
  6. Select “Open Payroll”


Edits, warnings, and exclusions:
  1. Editing employee payroll information
    1. Important Note- If errors in payroll information (compensation amount, hrs or ot hrs worked, benefit deduction totals, etc.) are noted in the Payroll Edit Page during entry, there are 2 options for resolution
      1. Make the change directly within the Payroll Edit screen- This will affect only the payroll information
        1. For instance, if hrs worked is updated for an employee within the Payroll Edit screen, that change will not reflect on the applicable timecard without a manual change to the timecard directly
      2. Make the change within the affected employee’s information
        1. Once the payroll information adjustment has been saved in the employee’s information and payroll has been resumed, a red exclamation mark should display by the Employee’s name
        2. Click the icon to view a Summary of the change in the Employee's information, and click "Update Employee" to apply the change to the Payroll Edit page

  2. Pause and resume payroll- Pause payroll at any point during the process and resume later without losing progress- All changes are automatically saved as you work
    1. Learn how to resume an open payroll here
  3. Payroll warnings- If any employees are missing crucial information, an error message will display in red at the top of the table

    2. Employees who are missing crucial information are unable to be included in the payroll run and will display in a disabled state 
    3. If an employee is missing information, such as their SSN, the information must be entered in their profile, and the payroll run must be reopened in order to include the employee in the payroll run
      1. To do so, scroll to the bottom of the screen and select “Start Over”
  4. Exclusions
    1. Payroll information- If certain payroll items do not need to be included for the pay period, they can easily be excluded- Simply check the "Skip for this pay period" box next to any component that should be excluded 
      1. The selected section will be hidden from view, and all related information will be automatically excluded from the payroll run.

        1. Earnings (beyond hourly/salary/PTO pay)
        2. Deductions
        3. Benefit Deductions
  5. Employees- Employees are listed alphabetically by their last name. Take a moment to ensure all employees who should be included are listed and selected
    1. If any employees should be excluded from the payroll run, use the checkbox beside their name to deselect them

Payroll information entry:
Work through each column of payroll information to review or enter in the appropriate pay information
  1. Compensation

    2. Salaried employees are listed with their per pay period compensation
    3. Hourly employees are listed with their hourly rate
    4. Employees with missing compensation information in BerniePortal will default to $0.00- Please review the yellow warning area for a list of employees with a $0.00 compensation, and make changes if necessary
    5. If changes need to be made to an employee’s compensation, make the change directly in the Payroll Edit screen or in the employee’s profile
  2. Overtime rate (OT Rate)

    2. Salaried/Exempt employees will not display an Overtime Rate 
    3. Hourly/Non-exempt employees will display their Hourly Overtime Rate (Rate per Hour * Overtime Factor)
    4. Employees with missing Overtime Factor information in BerniePortal will default to $0.00- Please review the yellow warning area for a list of employees with a $0.00 Overtime Rate, and make changes if necessary
    5. If changes need to be made to an employee’s OT Rate, make the change directly in the Payroll Edit screen or in the employee’s profile 
      1. An Employee’s Overtime rate can be configured in the “Other Info” section of their Employee Profile
  3. Hours (HRS)

    2. Salaried/Exempt employees will not display hours
    3. Hourly/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
      1. If an Employer does not utilize the BerniePortal Time and Attendance feature, hours can be entered manually
    4. If changes need to be made to an employee’s hours, make the change directly in the Payroll Edit screen or in the employee’s timecard 
  4. Overtime hours (OT Hours)

    2. Salaried/Exempt employees will not display Overtime Hours 
    3. Hourly/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 
      1. If an Employer does not utilize the BerniePortal Time and Attendance feature, OT hours can be entered manually
    4. If an employee’s overtime hours need to be edited, make the change directly in the Payroll Edit screen or in the employee’s timecard
  5. PTO (Paid Time Off Hours)

    2. Salaried/Exempt employees will not display PTO Hours as a payroll earning
      1. PTO balances will display on all check stubs, regardless
    3. Hourly/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
      1. If an Employer does not utilize the BerniePortal PTO feature, PTO hours can be entered manually
    4. If changes need to be made to an employee’s PTO hours, make the change directly in the Payroll Edit screen or in the employee’s profile
  6. Earnings

    2. Review employee “Earnings” by selecting the bubble beside that employee’s Earnings total
    3. Available Earning types will be listed- Type a value in the desired input field to add Earning amounts

      2. Select the “Recurring” checkbox beside an Earning type to repeat that Earning Type and Amount each pay period
      3. Select “I’m Done” to finalize
  7. Reimbursements

    2. Enter an employee's Reimbursement total in their "Reimbursements" field
    3. Reimbursements will display as a negative deduction in the Employee’s pay information- This ensures that the amount is fully refunded to the employee without including the payment in their taxable income
  8. Deductions

    2. Review employee “Deductions” by selecting the bubble beside that employee’s Deductions total
    3. Available Deduction types will be listed- Type a value in the desired input field to add Deduction amounts

      2. Select the “Recurring” checkbox beside a Deduction type to repeat that Deduction Type and Amount each pay period
      3. Select “I’m Done” to finalize
  9. Benefit deductions

    2. Review a breakdown of employee “Benefit Deductions” by selecting the bubble beside that employee’s Benefit Deductions total
    3. If adjustments are needed, make the change by benefit type or bucket, then select “I’m Done” 
      1. IMAGE
      2. Note that this does not update the employee’s Benefit Enrollment in BerniePortal-Changes are reflected for the payroll run only
      3. Benefit deduction amounts are pulled into payroll directly from the Employee’s enrollment within BerniePortal
      4. If there is an error, contact your Benefits Broker to assist with adjusting the benefits configuration within the Employer Portal appropriately 
  10. Gross total

    2. An employee’s Gross Total consists of their Compensation, Overtime Pay, PTO Pay, and Earnings
Save and review:
  1. Ensure that all appropriate employees are included/excluded, all employee information is correct, and that all Errors and Warnings have been resolved, then select “Save & Review”
    1. If you’d like a clean slate for the selected pay period, select “Start Over” 
    2. All progress will be cleared, and you can re-open a new payroll run for the applicable pay period 
  2. Download the PreProcess Report to review payroll run totals, as well as employee and employer tax information by clicking the blue "PreProcess Register" button on your Payroll Summary Page
    1. If you’d like to make further changes, select “Back to Edit”
    2. If all pay information is confirmed to be correct, select “Run Payroll” to begin processing the payroll run

Submit payroll: 
  1. Select “Run Payroll” within the Payroll Summary Page to submit payroll
    1. Employers will be prompted to confirm that they have reviewed the PreProcess Register for accuracy and approve all payment information for processing as documented

Post-submission important note:
  1. Once payroll is submitted, payment information becomes locked and cannot be modified
  2. If errors are discovered after submission, contact your account manager immediately for assistance with corrective actions

Need to run an off-cycle payroll run, for example, bonuses? Click here for information on submitting a request!

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