WPMU best practice

Can anyone please explain or direct me to documentation with detailed best practice for installing and using WPMU.

I want to set up a site that i can offer my team the option of a members area where they can apply for a blog through my site.

I currently have my main site at example.com (single install of WP) with a members link leading to example.com/members (where i have a multisite installed) on example.com/members i have all of the features that members can access once they register (with or without the option of their own blog) then once they register through example.com/members they then have the option then to get a blog of their own…

NOW, once they register they are getting the message “you already have example.com/members as one of your sites” which I don’t want, i DO however want them to be registered as a MEMBER of example.com/members so they can then access the content set aside for registered users only but not as someone with access to example.com/members admin area. (albeit they cant access site admin, they are being told they have access to example.com/members.

All I want to do is offer a section of the site where they can access the members only content and THEN give them a choice to get their own blog via the “wp-signup.php” page WITHOUT being given permissions for the example.com/members site.

I hope this makes sense so far.

It seems that I have to have it set up this way in order to be able to have a full custom website and content in the members area (example.com/members) as i have no idea how i can connect databases from the example.com (which is currently my main website and has NO need for user registration) and the example.com/members. I have a link that visitors would click located on example.com to be taken through to the members area but the actual registration page in located on example.com/members.

If anyone can assist i would be extremely grateful and if anyone needs to see what i mean then i can provide a link to the site and take it out of maintenance mode so you can get a better idea.

Thanks