Change the software to NOT allow a negative pay if a deduction plus taxes bring the net into a negative. Example: In other Payroll software if I pay someone and want to defer as much as possible of the gross, I feed in the gross, the same amount to be deferred and the system knows by priority to take the necessary taxes and then puts the balance towards the deferred deduction and leaves a zero balance. In your system, a lot of time is spent going back to the time entries and trying to back into the correct amount and recalculating the payroll.