Payroll separate checks


We are a co-existent shop, World 7.3 Cum 11, OneWorld 733.1 SP 7.1.

In our company, we issue some separate checks for various reasons, and when an employee has additional withholding set for federal taxes, we don't want this to be taken in these separate checks, only from the payroll check for hours worked. Anyone know how to accomplish this? If we set to supplemental, the taxes coming out are far greater than normal, leaving very little in the check. Any thoughts greatly appreciated.