I've been dealing with this same problem for eight years now. Quickbooks isn't capable of it. My first accounting program for the mac could handle it in 1988. I have had problems with missing the freight deduction for years. I am now adopting a new tactic of entering the invoice net of the freight for the FFA as it is our normal practice of paying within terms. That way the discount is taken properly and the freight is already deducted. If the vendor has a problem with the freight deduction they will contact you.  I hope this helps.