Not sure of all the features you are looking for but check out
http://www.adtrackplus.com might be what you are looking for. It allows you to do all your own payouts, print checks etc.
You can have multi-programs, multi-payout levels (sale or amount based plus other options) and can be customized. The person who wrote it is very helpful if you want knew features as well.
Just tell them I sent ya and see if you can get a discount.
Andy