Drake Accounting®: Why is an employee's bonus check showing a negative amount for Net Pay?
Double check the Taxing and Income Options selection for the benefit under Employees > Deductions & Benefits. If Taxed - Not Applied to Gross or Net Pay or Taxed - Apply to Gross Only are selected, this will cause a negative Net Pay amount to be produced.
Be sure to select Save And Apply All or update the benefit for each employee on the Employee Setup screen after making changes.