Yes, I make the roofs separately to sit on top of the building, with a low parapet on top made of strip balsa.
I went through a phase of having the roofs fit inside the walls, resting on a support. This was actually close to how the real things are built, and looks very good. Unfortunately, once the buildings are painted it was very hard to get the roof inserts out again, except if they were so loose to begin with that it was very obvious.
The buildings are all foamcore, pinned with ordinary dressmakers' pins as well as using white glue. the pins hold the walls 'square', and strengthen the joins.