so, I'm not sure if prosper or tracking pro can do this, but here's the traffic funnel I have set up:

Adwords (content and search) -> opt in landing page -> thank you page -> Clickbank offer -> Clickbank success

I also have people coming through Aweber to the affiliate offer.

If I could get the CB merchant to put my code on their thank you page, would this flow work?

Thx!

I don't know what you mean exactly.

Where is the CB thankyou page in your funnel? What code is "your code" that they should put? Are you referring to the tracking pixel? If so, then I say yes.