Membership plugin sync with sub-directories

I have the membership plugin working on the main site domain, but having problems recognizing the sub-directories. My sub-directory is an ecommerce site (not marketpress, yet) that does have it’s own login. Could it be conflicting with the membership login? What I’m trying to do is run a membership site that has the ecommerce and a Business Directory. The member signs in and then has access to the other 2 directories as well. I tried the URL Groups option, but that shut my members out as well. Any ideas?? This is not a Multisite, either. Could that be my problem? I’m in the process of setting this whole layout up as a Multisite with sub-domains, but need to get this first one up and running if possible.