I'm having trouble getting what your saying in the second paragraph. Is the city in the canyon?

Regardless, take a look at Sharn: City of Towers. Basically, build it into smaller flat sections which you can then stack up to make the "Tall City"

I'm having a bit of a problem with what you're trying to say as well. My understanding of it is thus:

-Canyon, 100 feet between cliff faces
-City built onto either side (or only one?) up to 50' tall
-Population approx. 500 (not so big, so easier to work with)

I list these out really only to clarify for myself what it is you're trying to describe. My method of mapping makes details fairly irrelevant.

If/when I have to map something that has multiple layers, I'll just make maps of the individual layers, with clearly marked rooms/passages/stairs/etc. All of them end up looking like floor-plans or blueprints, which isn't a problem generally speaking as long as you've noted somewhere the height of the storeys.

If you must have a map that displays every floor in relation to one another, I'd suggest having your ground floor drawn on standard paper, and the following storeys on rice paper/tracing paper, using a different color pen/marker for each floor.

Laying them all on top of one another will be mind numbingly confusing to look at, but it'll at least give you an idea of how the rooms line up with one another rather than having to compare multiple maps side by side.

That's not a bad suggestion. The other alternative I suppose would be just counting squares on graph paper. Perhaps it's just a lot of work and I"m whining. lol.