When you gain access to the Inner Chamber (Tower #2), take all three rings, red, blue, and green. When you get to the 4th trial, (maze that mixes up the controls), equip the blue ring and your controls will return to normal and you can proceed through the maze like you were playing an ordinary area. Once you step through the door at the end, remove the blue ring.
To get into the control room you must first get the Stone of Thirst from Dorn. Then go to the grave on the side of the Chapel door, the one blocked by wood that you can pull away. Use the Ring of the Dead to speak to the soul and then throw some Dragon's Tears on the grave. Speak to him again. He will tell you the Stone's incantation. Go to the reservoir (tunnels in excavation area 2) and use the Stone in the water. Climb down the ladder and up the ladder on the other side of the room. You are now in the Control Room!
You'll have to find the Fairy and Elf Statues to access the area where you'll find the Pixie Flute. The Fairy Statue is on the shelf near the entrance to Disciples' Tower. The Elf Statue is on a bar a little further inside the building. When you take the statues up the stairway in the Tower, Lakmir will stop you and talk to you. When he's finished, continue up the stairs where you will find Liquid Sunset and an Ancient Coin. You also will find a statue puzzle on a shelf, a perfect place to put your Fairy and Elf Statues. If you place them correctly, a staircase leading to the Pixie Flute will open.
You can find the Stone of Thirst inside Disciples' Tower, but you'll also have to get the Incantation for the Stone of Thirst to use it. In the Cathedral Courtyard, remove the boards that block a pathway, then continue to a grave. Use a Dragon Tears on the grave and equip the Ring of the Dead to raise him from his final resting place. (A ghost there will reward you with the Incantation for your trouble.) Head back to Disciples' Tower, then follow the red carpet inside to a door with an arrow on it. Go through the door then down the stairs. One of the doors in the hallway opens to a room with a bed, where you will be able to put your incantation to good use. Talk to Dorn, who has a valuable item. The Stone and Incantaion. It will allow you to drain the water form the reservoir, so you can access the Control Room.