I have to say that this screams out to be done as an isometric or perspective view (isometric will be clearer).

If you want to do top down you can make the regions clearly different in colour or style - after all the different vertical plateaus are likely to have different styles of houses on them - so the cliffs should clearly divide very different areas of the city. You can make the cliffs quite wide too so they clearly delineate the break between regions. Cliffs are very rarely perfectly vertical anyway. Then indicate the height change with text - +20' for example.