The affiliate program would need to be managed from a central location on the Central Store - so it would have to be integrated so that when we generate the feed to the Local Store, it would need to generate affiliate code for each feed. This the considerations that we would require in the development.
I was really wondering if any off the shelf products/plugins are already made for this purpose - I can't imagine that we would be the only ones that are going to be doing this... would save a HEAP of development time, that's for sure!
For building a professional ecommerce site it will better to talk to some professionals who have already deal some projects or sites and ask from few different peoples. They will come up with good suggestions and solutions to handle this , ways to promote and manage it.