Once you find the secret passage, pull the switch inside to open those big yellow slabs. Enter the now revealed door, and look for a switch. This will lower the pillar in the centre of the room to reveal the Emerald Key. Once you get the key, the big yellow slabs begin to move. Careful! It's a trap. You will get crushed by the slabs unless you run through when all of them are open. You need to time yourself carefully for this.
Note: one of the yellow doors in the room will open if you're playing deathmatch. The teleport inside takes you up to the top of the cliff outside the chapel, where there's an item or two. This only applies to deathmatch games, though. So far, I've not been able to open this area in single-player mode.
For those of you who wonder what those switches behind the fireball traps do... it's simple. Those switches simply re-activates the walls in case you get stuck behind them when they are deactivated. The switches don't do anything when the trap is active.
Tip: there's a platinum helmet somewhere on the battlements which will increase your armor class: see if you can find it!
Now, enter the courtyard with the bell tower. Somewhere on the right is the entrance to the cave with the silver key. Be careful once you get the key, though, because another trap will be activated. The easiest way to get out is to step in front of the first crusher, and when it slams together, run forward against it. Once it opens, you'll be running against the second crusher, and so on. This works because of the way the crushers are timed.
Note: I noticed that with the Mage, there's a bug here that lets you shoot at the bell from outside, without ever getting the Silver Key. It's a little harder than in the Demo version of Hexen, but it's still possible. I wonder if this is a slip by the level designers.
Now simply go back to the chapel and step into the teleport, which will take you to a small room with the portal leading to the next level, the Seven Portals. Stepping close to the portal opens a passage to the right that leads back to the front of the chapel.