Keys are used automatically when you click on the corresponding locked chest or door.
For the two tombs, you can only unlock one of them, but they both lead to the same place so it doesn't matter which one is opened and which one remains locked.
After entering one of the tombs and getting to the forth level, there are stairs in the south west corner to the fifth level. You can get the second teleporter pyramid on the forth level, if you didn't already use the first to get to it.