Situation: Shop owner (logged in) Subscriber of main site.

Situation:
Shop owner (logged in) Subscriber of main site. Administrator of their own shop.

If they are viewing the main site http://www.site.com their admin bar options will redirect them to a subscriber back end. If they are viewing their site and use their admin bar links they are directed to the correct back end of their shops site.

How can I fix this issue and have them always only be using their correct back end?

Also how will this effect shoppers? I want every to go to their correct back end at all times.

It's just a little confusing. Any ideas?