You can create a pay element for deduction, and insert this into his pay records to deduct the amount. The system allows a negative amount in the pay records and in the reports.
Please follow the steps below to create the pay element:
Go to the Payroll module.
Click Pay Element Setup and click New.
Enter a Pay Element ID, e.g. Miscellaneous deductions and select Deductions.
Click Next and select None of the above.
Click Next and select Standard Deduction.
Click Next, select Free, and click Finish.
In the property screen, remove the Subject to SDF and Subject to Ordinary. (arrow over to the left)
From the left panel, select Non-Taxable Code and arrow over to the right.
Go to Pay Records and double-click the affected employee.
Insert the pay element that you have created.