If a user is registered on Stack Overflow, and Super User, does s/he still get the 100 bonus points? If the bonus points are given to users who have a minimal reputation (I don't recall it was the case, when I get the bonus points), what happens to users who didn't reach the required reputation? Do they get the bonus points when they reach 200 points of reputation?
When you associate one or more sites that have 200+ rep, you get a single +100 point bonus on the new site.
It doesn't matter how many other sites you belong to with 200+ rep; if you earn 200 rep on any single site, you get a 100-point bonus on each new site you sign up for from then on.
But you can't get more than 100 points as the result of associating other account(s) on any given site.
EDIT: You don't automatically get the points if you didn't have the 200 minimum on another site when you associated your account(s), but then you hit it later. If that occurs, you have to disassociate the account that has hit the threshold, and then re-associate it now that you meet the criteria.
(But if the part answered in the edit is the crux of what you were asking, then I think I agree with @Popular Demand above - your question is likely a dupe of one of a couple of questions.