Below are 2 reasons that a net pay can results as a negative amount:
  1. Marital status (employee data item .MARITAL) is missing from the Payroll Calculation tab of the employee record.

           How to correct

              a.  If this is the first payroll check for a new employee, review the Payroll Calculation tab for Marital status.  If it is missing, add the status and then perform Net Pay Calculation again.
              b.  Marital status is required for all employees subject to Federal Withholding.  If an employee is claiming exempt from withholding on Form W-4, Marital status is still required on the Payroll Calculation tab.
 
  1. Small gross pay due to shortened work schedule; calculated deductions are in excess of gross pay.

           How to correct

              a.  You need to enter negative one-time deductions to offset the negative net pay.
              b.  Your organization needs to decide how the employee is to re-pay the offset deductions.

                             i.   If the employee is expected to receive normal paychecks in the future, the offset can be deducted from the next check.
                             ii.  If this is the employee's final paycheck, if the offset is for future benefits (e.g. health insurance for the next month), no further action is required if the benefit ends with employment.  
                             iii. If this is the employee's final paycheck and the offset is for benefits already received, a method of setting up a receivable from the employee and billing the employee separately needs to be determined.