First, you'll need the developer's license (although you probably figured that out).  For this project, as long as all of these user sites are under your single domain name — you should be just fine.

You also asked how you can setup our "affiliate program", however I don't understand what you mean with that.

As far as different visual themes, Market has an options area that allows a user to select their own logo, header colors, and navigational colors.  Currently there are not mulitiple theme variations beyond that.