Please guide!

Hi,In my WPMS,I'm running affiliates so people can earn money for referring Paid(supporter blog) signups.
My question is,is there any way so supports can have their own paid membership system(through membership plugin) and have their own affiliate system running as well?As I can see membership is supported by affiliate plugin but would that be usable in per site basis?
If yes,then can you please guide me how to set that up?
Many thanks in advance.