[iThemes Exchange Membership] multiple site management advice

I’m looking for some advice on how to handle this situation:

I am not a developer, but my job is requiring me to build a membership site using iThemes Exchange with the Membership plugin.

I have a primary domain (Primary) with a dreamweaver website and subdomain (Book1) with my the wordpress website. We sell an online book (hosted on Book1) and a number of physical products and digital downloads.

Currently, to gain access to Book1 you purchase a membership through the “store” on Book1. All other products have to be purchased through a godaddy shopping cart on Primary. I anticipate there will also be an additional online book (with its own membership restrictions) in the future.

I would really like to have one central shopping cart through Primary (I plan to rebuild this website in wordpress), but iThemes Exchange can only restrict membership on the site on which it is installed. This means that our users would have to go to multiple sites in order to make their purchases. I am wondering if anyone out there with greater wordpress mojo than I can help me out with a creative way to work around this in wordpress.

I’ve done a lot of reading about wordpress multi-sites, but I’m not quiet sure I understand it well enough to discern whether or not it would solve my problem. Thoughts?

Would subfolders/subdirectories function any differently than the current subdomain set-up?

Ideally, each site (Primary, Book1, and – eventually – Book2) would have their own unique branding. Although I like that Primary and Book1 are completely separate right now, the best possible solution I’ve come up with is to dump the contents from all the sites into a single site and use unique headers to distinguish/brand the different “site” sections. This seems messy and hurts my order-loving brain, though. 🙂

Any advice would be greatly appreciated!