Membership site with sub-domains or sub-directories

I'm setting up a Membership site that requires e-commerce for product sales and a business directory for members to access. Will the single Membership plugin work for limiting access to paying members for the main site, e-commerce and business directory?
If each plugin requires it's own blog, what would work best for the single Membership plugin to handle everything, sub-domain or sub-directory? Also, is a MU site required? I just upgraded hoping to keep all the Themes and Plugins coming from one source!