Looks like you have a lot of space to work with! The first picture of the elevated tracks crossing over lower level tracks looks ripe for a scene with retaining walls and city styled tunnels. A lot of city scenes I've seen have the buildings on a level a little higher than the tracks with retaiing walls or rock cuts along the trackline. They look convincing to me.
That track that goes from 1/2 inch to 1 inch on the right side of your plan is at a lower elevation than the track that I presume is at the front of the benchwork, right? (the line that goes from 2 1/2" to 2"). Maybe that elevated track could be put on girders and bridge supports so you could see (and access) the lower level track behind it. Then build a retaining wall to the right of the lower track to use as a foundation for the city creating a "concrete canyon" for your trains to run through. Otherwise maybe you could cover the lower level track with buildings to disuise the loop so only the upper level was immediately visible. Hmmmmm, all kinds of possibilities!
Ralph