Could 3-4 subsites work together with WPMU Dev Affiliate plugin without separation?

Now I am studying to work for my entire website affiliate business model.

Question 1:
If my project is to be online teaching with 3 or 4 sub-sites (sub1-4.sitename.com), could WPMU Dev Affiliate plugin work for these 3 or 4 sub-sites together with the main site (sitename.com) as non-separated affiliate program?

Question 2:
After some reading from WPMU Dev, Pro Sites could be a nice and successful business model for me. Anyway, I am focusing on online teaching (e-learning) with serious Multi-DB requirement. Different levels of knowledge should be designed to store in different mysql table. Otherwise, all could be a big mass in the future. To resolve affiliate all-in- one function is quite important for marketing efficiency and save my time.

This meant I just offer myself an affiliate program with my 3-4 "schools" each is a wordpress sub-blog. Could you help me to confirm if WPMU Dev Affiliate plugin could work for 3-4 sub-sites together with the main site as one without separation?