Josh,

What site are you running an affiliate program for? Usually for people looking to sell affiliate products, they follow the 3 minute guide in the how to section of the forums (hidden to unregistered users), which redirects the buy now button to the affiliate link provided by the site. In your case it sounds like you don't have one? It still should be able to work though, as you can still set the return url after purchase in the code itself, and if the php code you require is there, there shouldn't be any problems.

-aj

Not directly. You would need to use something like E-Junkie's cart to run your own affiliate program on your own site. Also, this question along with your developer license question makes me want to point out that even with a devleoper license, Market can not simply be resold as is. EX: You buy a developer license and plan on selling the theme and running and affiliate program for it without making any modifications is a no-no. The developers licenses allows you to use Market as a base and build client work upon it, saving you time and money. It does not give you rights to package the theme and sell it as your own. I'm in no way saying you were going to do this, I just wanted to make it clear.