The amount submitted using the Additional Pay forms is the total/gross amount, not including any taxes and deductions that will be subtracted when payroll is processed.
The forms have a Gross-Up checkbox to indicate that the submitted amount should be the net amount that should be paid to the employee; if this checkbox is selected, the employee will receive the submitted amount exactly as their net amount and the department/chartstring will be charged for the additional amounts that would have gotten taken out in taxes/deductions (i.e., the true gross amount needed for the employee to get paid that amount as net).