Buffan, shut up and read the rules. You're allowed to have 46 (I think) active players, plus an emergency QB. He's basically listed as inactive, and doesn't take up a roster spot on gameday. He's there so that if something happens to the top two guys, you still have a QB. You are not, on the other hand, allowed to use him as a substitute - 1 didn't work, and 2 didn't work, let's try 3. To prevent that and phony injuries to allow it otherwise, the NFL says the top two guys can't go back in if the 3rd guy plays.
It's the damn rule, and it's special for QBs. So stop being a spazz.