After activating the western switch in the "ring" in the water flooded area, the door to the round building in the south east courtyard will open. Activate the switch inside, which will raise some stairs north of you. Push the back side of the switch upstairs: the ledge west of the stairs (where the combat armor is placed) will temporarily lower, revealing a secret area (Sector 83) as well releasing the six Chaingunners inside. If you are caught in the secret area, push the metal part of the western wall, will release an arch-vile. Acitvate the switch in his hideout to temporarily lower the ledge again.
Crossing the line from the raised bridge to the solid part of the inner "ring" where the eastern switch is placed will reveal a Megasphere (Sector 282) which can be seen from the lift in the south of the ring. Ride the that lift up and look to the south. At that part of the map you will know how to get there.
After activating the northern switch in the "ring" in the water flooded area, a Soul Sphere will be revealed: climb the stairs east of the round building in the south east courtyard (mentioned in secret 1) and follow the hallway to the room on the east side. In it's south side you will find an alcove containing the Soul Sphere. (Sector 280)
After activating the northern switch in the "ring" in the water flooded area, another Soul Sphere will be revealed: It is in an alcove in the south wall on the ledge west of you. (Sector 284) At that part of the map you will know how to get there.
Activating the switch mentioned in secret 4 also opens a new area: From the water flooded starting area, pass the northern door and climb the eastern stairs. A triangle shaped passage containig some enemies is now available in the north east of that room. In the north of it is a switch. Push the wall west of that switch to reveal a secret passage (Sector 242) containing 2 more chaingunners.
This Secret is available from the beginning of the map without activating any more switches, so you can collect it first if you want: From secret 5 walk back in the main rectangular room. Push the northern wall east of stairs and west of the triangle shaped passage. The wall will lower, allowing you to access a secret passage containing 16 Chaingunners and two Stimpacks (Sector 170).