Levels were designed to let you do that.
Of course, it won't be as easy as if you had to design a classic house with two stories or levels on top of each other, but if you pay attention to the elevation of each level and the height of the walls you add to the levels, you can achieve the kind of design you look for. As explained in the included help, keep in mind that you can create underground levels by setting their elevation with a negative a value.