I am using "Easy Click Mate" which is an affiliate manager program which is specifically geared to selling Clickbank products. The reason that I have choosen that program is that I want all of my payments to my affiliates to happen automatically.
ECM has all the functionality that you have already described. I am in the process of incorporating the program to also track sales via paypal (since a lot of people consider paypal money to be funny money). So far the program is working wonderfully.