Carl, I am just beginning to understand multi-store setup myself. But I do know that you can set up users for each store and restrict those users to what they can access.
It is found in System > Users and then you can setup User groups and/or users.
That gives the Master Admin control.
Additionally you can control any of the categories, products etc by either having the checkbox for the store on or off.
So if you have product 1 and select Store A and Store B, both will see product 1, but they can each set their own pricing.
If you have product 1 and only select Store A, Store B won't see it in their products listing.
Now what I am still looking to figure out is if Store A sees there is Store B in the dropdowns. I think they do, but haven't tested completely yet.
Hope this helps a bit.