When supplemental checks are created, you can use the options selected in the Calculate Payroll view instead of using the employee settings and payroll system settings. 

Situations when payroll settings may need to be overridden to create supplemental checks: 

• Bonus payments. If an employee is receiving a bonus or incentive pay separate from their regular payroll check, a supplemental check ensures these payments are processed correctly, often with a different tax withholding rate. 

• Expense reimbursements. If an employee is getting reimbursed for business expenses, a separate check may be needed to avoid mixing taxable and non-taxable payments. 

• Correction of payroll errors. If a mistake occurred in a previous payroll check (for example, mixing overtime or underpayment), a supplemental check allows for quick correction without waiting for the next payroll cycle. 

• Severance or special payments. Payments like severance, retroactive pay increases, or settlement payments are sometimes processed separately for tracking and tax purposes. 

• Different tax treatment. The IRS allows flat-rate withholding (22% for federal taxes in the U.S.) on supplemental wages, which may differ from  the employee's regular withholding method. This is useful when processes bonuses or lump-sum payments. 

• Manual payroll adjustments. If an automated payroll settings don't support a specific payment scenario, an override allows manual adjustments to ensure accurate pay. 

 

This option is available in the 2025.02 release. 

 

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Override payroll settings on supplemental checks

1. Open Connect Payroll > Employees > Calculate Payroll. 

2. Click Options  (F12). 

3. In the Supplemental Checks section, click to select Override payroll settings. 

 

4. Set up the supplemental check override options. 

Deactivate direct deposit

Create a paper payroll check instead of using an electronic transfer to deposit the supplemental check amount. Selecting this option will disable direct deposit and the net pay amount will be assigned to the net type pay code. 

Monthly period number

Override the monthly period number with a new monthly period number. 

Some employers choose to issue supplement checks (for example, bonuses, commissions) in a different monthly period to take advantage of different tax rates or to avoid pushing the employee into a higher tax bracket for a particular month. 

If a correction, bonus, or other supplemental payment is needed after the regular payroll is processed, issuing it in the next period ensures timely payment without disrupting normal payroll runs. 

Tax rate

Set up this section to use an override tax rate to calculate supplemental checks. 

• To override the federal tax rate, click to select Federal withholding rate, and then enter the federal tax rate for calculating a supplemental check.

• To override the state tax rate, click to select State withholding rate, and then enter the state tax rate for calculating a supplemental check. 

 

5. Click OK.  

 

 

 

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