- Add a payment at the Payment on Account screen, and enter the amount of the payroll deduction in the Discount Amount field.
- Change the Discount G/L Account to the same G/L Account that was used for the Payroll Deduction. If you don't know which general ledger account this is, it can be found at File / Open / Employees / Deductions.
- In the grid, enter the amount in the Discount column and click Apply to zero out the Payment column for the invoice(s) you want to pay with the payroll deduction.
- Save the payment.
Another option is to set up a new payment method (Accounting / Setup / Pay Methods) pointing to the payroll deduction G/L account, and use that payment method to pay the employee's invoices.
