Maybe this will help other GMs:
In the Doomsday Stores proper, the area labeled G4 is NOT G4 but a part of G3. G4 is the unlabeled continuation of this walkway (turning into stairs and a ramp) inside the inner sphere.
You will want to decide how high the bridge falsely labeled as G4 is above the water. I recommend putting it at water level with 20' of air above it but none below, to help out the aboleths.
The area inside G5 and outside G6 is drawn to resemble stone flooring, but the text makes it clear that this is open air above water (held out by a water-only force field). G6 itself is a stone platform but the area surrounding it is NOT.
The inexplicable inset on the map of this level is a side view. This makes it clear that G6 is not at the level of, nor attached to, the top of the stair/ramp of (unlabeled) G4 but is far above it. The exact position of the stairs can't be reconciled between the inset map and the main map. I'd go with the main map.
Despite the map being drawn with nothing outside the other 7 doors of G1, there are passages there leading to other doomsday devices, as described in the epilogue. You aren't supposed to be able to get in there during the main action, though. (Good luck with that. My PCs always go where they are not supposed to go.)
Having said many grumpy things, I will say that I do really like this as a setting for a fight, and the idea of the complex "dumping core" and flooding to shut down is nicely flavorful. I just wish it didn't take 20 minutes of re-reading (and, alas, asking for help from my player) to figure out the map....