Its been a long time, but generally the way I used to think about it was like taking a bed sheet and dropping it over your level. Characters can only move and path-find on the surface of the sheet itself, so anything that was multiple floors or went under something else (like trying to do a bridge) would not actually work right and could only be interacted with on the top most level. Ceilings were handled with flat black 3D planes that were non physical that were destroyed when some trigger event occurred (like covering something with a piece of paper, and then removing the paper to expose it).
You could try and get tricky and do a level where all the upper areas didn't sit on top of the lower areas and try to fake some stuff with creative use of those planes and trigger areas but that's just a fancy version of the robot factory really... or you could try something like The Matrix Mod did (I think that was the one) that actually had multiple rooms on a single map on a single plane (with each one surrounded by a lot of black empty space so you couldn't see the other parts of the level when in one of them), and when you entered a new area through a portal of some kind (door, elevator etc...), the camera and characters would be transported to another part of the map containing the "new" level - basically instantaneous area hopping on a single map similar in concept to the ffx freeroam mod. The illusion broke if you had your camera zoom levels set to go out really wide though.