Entering benefit information for each employee

My non profit is beginning to offer a benefit plan for some employees.  i can not figure out how to enter the taxable benefit setting and the amount to deduct from the employees income, which are different amounts.  If i enter a benefit amount in the Income tab and a different amount in the deduction tab, the pay stub adds the benefit to the income amount and subtracts the same amount from the gross pay, not the deduction amount.  Also, neither amount shows up in the journal entry.  Curious.