Again, step out of the room with the three portals into the one with the big door. The door slowly opens, revealing the main room of the chapel. Before going in, you might want to jump on the dragon-wall ledges to your left and right and grab whatever goodies are there. Be careful as this causes a couple of afrits to jump from the ceiling and attack you.
In the main chapel, kill all the monsters on the ground but if you're not feeling like it, leave the monsters and all the pillars and ledges be. It might be a bit stressing to always have to dodge their attacks but before long, you'll get on those ledges as well and killing them will be much easier. Go all the way north through the main room until you reach the platform with the small swamp pond (beware of the stalker there). Stepping on the platform causes the two pillars there to open, revealing a goodie and a Dark disciple each. It also opened two corridors in the walls (eastern and western) roughly in the middle of the main room. First go through the eastern corridor. If you have already been to the Wolf Chapel, as I recommended you, the way south should be opened (don't worry about the northern corridor, it will open later on). At the end of the southern corridor is a dragon-face wall. It serves as a lift and takes you to one of the ledges in the main room. Of that ledge jump down to the closest ledge just a bit north of and below you. When you are there, the wall behind you will open, releasing some monsters but also revealing a switch, the second part of the puzzle. Pull it, kill all the monsters on the pillars and ledges (now you're on the same height with them, killing them is much easier). and jump back down. Then go through the western corridor. There, it's all the same: it splits north and south with the northern corridor being blocked by rotating pillars (be careful about them, they are quite dangerous). Also don't miss the third part of the puzzle, placed right in the corridor when you enter it, even before it splits into two! Then go through the southern corridor. At the end, you'll notice two small parts of the wall with a different texture. Each is a lift that takes you to a ledge with some mana and monsters (again - from there it is easy to kill the slaughtaur on the pillar in this part of the room...).
The last puzzle-switch in this chapel is going to have to wait for your next visit, so now, head back to the Wolf Chapel...
Get to the corridors on the eastern and western side in the middle of the central hall. In each of them, a small room in the back (east and west, respectively) will have opened with some monsters in there. But, more importantly, both previously blocked corridors going north are now opened. So, first let's take the eastern one. This one leads you through a flight of stairs to a platform. When you'll reach it, a wall behind you will open, releasing Dark Disciples, so be careful. On your way back down, you can use the dragon-wall which lifts you to another platform with some monsters and mana. Now, go to the western corridor and also take the newly opened northern part. It leads you to a room in which is a small niche with a wall with a different pattern. It can be lowered and will take you up on a platform. There, you can open the dragon-wall, revealing more stairs going to another platform with a switch at the end. Pull it. Now get back down (the easiest way is simply to fall down) and again through the western corridor and then north. The dragon-wall in the northern end of the room is now open, revealing stairs going down. Follow the stairs, killing all the monsters as you go. Eventually, you'll find yourself in a corridor going around a swamp (beware of the spitting stalkers!). At the end of it is a switch - yes, THE FINAL switch, the NINTH part of the puzzle. If you want to collect some more goodies before leaving this level, you can get to the swamp you saw through the window. Just step into the small swamp pond in the main hall of the level and hit the wall with all the candles. The pond will lower down, opening a way into the swamp. Get rid of all the stalkers and gather up the goodies. To get back up, just hit the swamp-textured wall where you came from, it will lower and lift you again into the main hall.
And now, just get back to the Heresiarch's Seminary to fight the boss, the Heresiarch himself!