Affiliates with redirected sites

In order to meet the needs of a client to work with multiple currencies in a store we created a redirect to another store on another domain.

But now he pointed out that he wants to provide affiliates. So I installed Affiliates.

But now I’m wondering what will happen with the commission made in “the other” store. Will it work when people are just redirected to the homepage of the main site?

If not could you help me out with some smart ideas?

So what I want to happen is a multi currency store and affiliates that works on both currencies. Bur since this is a international company it is hard to tell what the buyers in the end will use as their currency.

I hope my question is clear…