In theory you can create as many layers as you want but you should limit yourself to only using four because It maxes your file a lot clearer and it's the right way to do it.
Generally you should avoid turning tiles because it messes up a lot
With the PRO basic tileset there is no way to make this right so you should avoid doing those kind of structures.
When doing mountains, you should try to keep it "closed" (I know it's not very clear but I can't find a better word)