You can enter fee waivers when you enter payment.  There is a field called wavier amount this is where the amount of the waiver should be entered.  In our calculations to find discrepancies we add the amount paid and the wavier amount and compare it to the amount owed.  If they are equal there is not a discrepancy. 

You could also change the amount owed.  We do not recommend this as it will adversely effect some reports.  In particular the Registration Overview/Finance Report displays the total amount of fee waivers your school has given.  This is calculated by adding all of the individual waiver amounts together.  If you modify the amount due instead of the entering a waiver amount this Total Wavier calculation will be meaningless.