What I was driving at was that, if you designed the layout along the same principles as the Berlin Anhalter project, you would (or should) end up with a lengthy route arranged in a sort of oval spiral. In the space you have available to you, I'd say this is well worth having a go. It would achieve the two or three levels you want in an unbroken run.
This would give you the sensation of seeing the trains appear to travel from station to station, running through open sections of line, just as they do when FREMO enthusiasts have a massive get-together and connect loads of different modules together to form a network.