I have killed Xydusa in the chamber right after doing the thing at the brazier. I have gone into her chamber and killed her. I then see a wheel with a switch. When I pull the switch the door behind where Xydusa was doing and that is a dead end. I can't go through the other door, what should I do?

There should be a switch of some kind in that hallway, just before you reach the barred door, that leads back to the Altar room I believe. You can only reach it from that side, although you could see it from the Altar room.

If you are talking about the Naga, you will need to go to the room that has the fountain in it. Look above the fountain, and you will see a lever. Go back the way you came, and you will see a new passage. You must be prepared to go slightly insane with the elevator maze that is here.