I found some kind of altar on the second chamber. How do I use it? What can it do? When I interact with it with E, it just says it's empty, regardless of what weapon I have equipped or anything I do in the room.
Have you been to the Oubliette yet? If not, that's a whole 'nother problem.
If you make it to the Oubliette, you'll find:
A room that contains a special piece of armor, the "Old Crest." This lays on TOP of any other armor you have or get afterwards. If you take one hit, it's gone. I suggest killing the boss before you pick it up, as then all you have to do is survive the second floor to find the altar without getting hit...
If you can find and bring the item to the altar:
You'll unlock a staircase to the second secret level, "Abbey of the True Gun"
Doing this is easier said than done...