How to Pay Employees with a Salary
Go to Payroll > Run a New Payroll.
On payroll Step 1: Payroll Entry, all active salaried employees will appear in the employee list.
Under the “Pay Salary” column, each salaried employee will have a checkbox.
This checkbox is automatically selected, meaning the employee’s full flat-dollar salary will be included in payroll.
To exclude a salaried employee from receiving their regular pay, simply uncheck the box.
Add Hours
If your state requires payroll hours for reporting or if you have set up time off accrual rules, hours will be mandatory.
💡 Salaried employee pay does not change based on the hours entered.
Add extra pay as needed (e.g., bonuses or additional earnings) in addition to their regular salary.
Use the “Off Cycle Payroll” in the Pay Schedule drop down to pay salaried employees ONLY a bonus or payroll that is not in the normal payroll run. See our help article, “How to Run an Off-cycle Payroll,” for more info.
Paying a Partial Salary
If an employee took unpaid time off and should receive a reduced salary, you have two options:
Option 1: Temporarily Adjust the Salary Rate
Go to the employee’s Pay Info tab. Payroll > Employee list > {select the employee name} > Pay Info.
Edit their salary to reflect the lower amount.
Run payroll.
After payroll is complete, change the salary back to the original amount.
Calculate the temporary salary:
Determine the employee’s hourly rate:
Hourly rate = Normal salary ÷ Total hours in the pay period(e.g., 80 hours for biweekly).Multiply the hourly rate by the hours worked to calculate the temporary salary.
Option 2: Use a Custom Money Type
Create a new Money Type specifically for partial salary payments. Settings > Payroll > Hours and Money Types.
Click +Add New
Name your money type something that will allow you and the employee to easily identify it, ex: “Partial Salary.”
In payroll:
Uncheck the “Pay Salary” box to prevent full salary payment.
Enter the partial salary amount in the custom Money Type field.