The different rooms connect through doors and are considered inaccessible up until when the doors are opened.
What this means is that the Overseers minions won't be moving across rooms because of closed doors.
Once the doors are opened though, the aliens can move freely among all connected (opened doors) rooms for tactical manoeuvring.
So what that means is that once you hit the crisis point, the Overseer opens one door to connect to the already explored (by the military guys) portion of the map, resolves the cards, which means that most likely he/she will have available aliens that aren't under immediate threat by the other players and thus will be able to plan a more efficient attack.
I hope this makes sense?
Wow, thanks for the quick reply. Yes, it helps clear things up alot. I guess I was not familiar with the term hidden room. Thought it would be more like unexplored room or something.