This is gonna be a short answer because I have been doing library for a very long time. You just cant know which ones you have already killed unless you have killed the final boss. The final boss is the only one that makes a change because it gives you an achievement first time you complete it "library liberator".
If I may do a suggestion that might help you. Start with the hardest one and test. You cant get into the room with the lever unless you have killed all the bosses.