Floors are exclusively for ceilings if it's on other floors. I may add a feature to add floors but that might cause some troubles with how it all works. So, you need to place a wall on the first floor there. The map building is essentially 2d, as in Doom, so no rooms above rooms explicitly allowed. You can place a custom tile though, no problems. Just wait for the next update when I add a feature allowing selecting which floor a custom tile will affect.