I have several areas that are like this. I simply put it on the floor the room is on. However I think it would depend on your situation on what your choice is. If the height of the AP matches an upper floor it would be a closer match to the real heat map, or interference map to be truthful. You cannot make the AP show on more than one map so you are stuck with picking one. Unless I have missed something the mapping does not do much to take in account the floors as far as what is shown on the real maps (not planning). It is almost as if you are dealing with each floor as a seperate building. The system does not think in 3D, at least HM Classic doesn't.
So I would ask do you want the map to show what the AP sees or what the client sees? If AP put it on the floor that matches the level of the AP. If client put it on the floor the client is on.