Pop-up window: I beleive that is controlled in the options in game with tool tips or something. Not sure exactly where, as I've had it set for so long to off, I forget.
Roofs: as a general guidline roofs usually start from +20 from the ground level per floor. so a first floor roof would start at 20, second floor, 40. This is the outside edge of the roof. the center peak will depend on how large the building is.
I'm sure Sydius will reply with his wisdom since this is one of his "specialties" *ahem*
Also, check out his FAQ for more general info.
-Ryandor