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!