Problem with WordPress User Registration

I have created a website with WordPrss 3.01. It is at http://www.art2stem.org/home. This site has 10 subsites (art2stem.org/apollo, for example). This site is for a School System "Club". This club has a main site (for overall general information and such) and then each school has it's own "club site". The school administrators need access to the main site (to be able to add/edit/remove content), the "coaches" of each club need access to only their club site (art2stem.org/apollo, for example). I have created the site and the sub sites and am now trying to grant access to the individual coaches to their sites. I tried to add a user via the backend "new user" and that did not work properly - the user was given a name of "unverified_367ef658". So I logged out of the site, went to the subsite (art2stem.org/apollo) and clicked "register", I entered a username and email address. I was able to register this way, but the person is now registered for the MAIN site (art2stem.org) NOT the sub site (art2stem.org/apollo). I have spent weeks on this project, have I set this up completely wrong?

I really need some help with this as quickly as possible. This site is set to go live on Friday August 20th.