I can think of two good examples of the sort of discreet cross section of z-layers that you're talking about. The first is the various The Sims games. Each floor of a house is a different z-layer, and movement between them is done via icons on the interface, and (I believe) shortcut keys. In The Sims, the only points where movement between levels was possible was stairs, which were visible if you were "above" (on the second floor) or "below" (on the first floor) them. The stairs can problems if you're trying to click on something behind them, but it's possible to rotate the camera to solve that issue. The only real source of confusion in this case would have been if a Sim was on the second floor, and you/the camera was on the first floor. The Sim would effectively disappear from view. However, this is solved by allowing the player to double click on a Sim's portrait in the interface to zoom right to them. For the first Sims game, you only had access to 2 floors, so it was generally pretty easy for people to keep track of the 8 maximum people in a 2 story household.
The other example is Simutrans, a freeware transportation simulator. In some ways, the game is similar to Rollercoaster Tycoon, in that you can cut through the landscape at will, and go underground with the push of a button. The only different is that each z-layer can be "sliced", so that you only see what's on that layer (and maybe a minimal bit of the terrain above), you can see a bit of this here. Overall, this prevents confusion in terms of selecting objects and building underground, but it can be confusing for newer players, and it's harder to get an overview of everything that is going on. However, a game like Simutrans doesn't require as much micromanagement as The Sims, so it's generally fine to miss out on a bit of the overview. Again, moving between levels is simply a matter of using the keyboard/interface, and due to being able to rotate the camera, most other problems are solved as well.
Overall, the exact solution is going to depend on the game. The Sim City series (except the first one) had various underground views to build pipes and subways, effectively separating the views from each other. Most games take this route, sometimes providing a simplistic version of the aboveground, so you generally know where you are, but it's still fairly well hidden. Others, like Rollercoaster Tycoon simply hide the terrain and let you build underground with everything else in full (transparent) sight. It can easily get confusing, though this can be helped with a "currently building here" tile highlighted. My own game uses the "slice" technique, showing only the current floor to the user, while allowing them to see the walls of everything below the current floor. Exactly how to handle the floors above them, I'm still trying to figure out, though I have a few different ideas.