You shouldn't be able to use their resuply bases, as you need a Military Alliance and above to do that. Likewise, you shouldn't see their systems, since you need to be a Partner with them.
Protectorate/SubVersion are treaties below Trade Alliance (and above), so it means you have a neutral relationship with the given Empire. However, I say "should" because I have yet to try this treaty. When an Empire is desperate enough to accept such a treaty, I am often able to... erh, borrow its planets with ease.
I should also say what a Subjugation treaty is supposed to do at least. It means the targeted Empire can no longer have any other treaty, they give you an important portion of their resources, and they share every technological discovery with you. That's quite a lot, but not many Empires are likely to comply with this kind of "agreement".
[ October 01, 2003, 21:08: Message edited by: Alneyan ]