Help with multisite install

I have purchased the Pro version of this plugin.

I am not running a blog farm. I have a main site and 4 subsites all controlled by admin. I would like to do a setup, whereby a user signs up and depending on their level have access to one or more/all subsites which are being run as subdirectories, not subdomains.

A new user can sign-up/login from either of the subsites or the main site. In other words com in via mydomain.com, mydomain.com/subdomain1, mydomain.com/subdomain2, etc.

Sign up and login are run by my theme.

My theme is dynamic and uses post types, post type indexes, taxonomies, taxonomy indexes, etc. to run and not that many pages. Some of the content I want to restrict are URI based. My problem is that while I can restrict URI’s on the main site it won’t restrict URI’s on subsites.

I am little confused about set up. do I need to set up levels on each subsite or just the main site or all? In which case will each subsite have it’s own MOP or do they all refer to the main site. I suspect the former, because of the pages I can choose from the one on the main site doesn’t come up.

At the end of the day I want to control all access to subsites via the main site and refer to the main site when a user hits a ‘wall’. Can this be done easily without needing to API script?

Thanks

https://wordpress.org/plugins/s2member/