Sorry if it' a bit confusing. I'll do my best to explain it

The catacombs are laid out in a rectangle like formation with a room on the bottom left, bottom right, top left and top right. You can enter the rooms on the top left and top right but there isn't much to do in there except look at coffins, at first. If you try opening the door on the bottom left, you will see a message which displays you need to get the key of the Great Leader and the Great Smither.
Once you have seen that message, visit the room on the top left and check the signs next to the coffins in each room, when you see the sign that says 'he was known for his great leading skills', then check inside that coffin and you will get the Leader Key. Head into the top right room as well and do the same to get the Smither Key.
Once you have both Keys head back to the room on the bottom left and it shall unlock for you. Inside of that room, check all of the bookshelves and you shall find the Master Key which should open up the room in the lower right side. Once in there, make good use of the healing point in the bottom right corner of the room and save your game, as you'll be taking on a big boss fight soon

Let me know if that helps!