#1 It's best in practice not to overlap your brushes. If you do it a couple times its not the end of the world. But it could cause some compile errors, portal saw into cluster or something like that.
#2 Even though a player can't see the roof of a building the texture will still be rendered unless you tell it not to be. So for optimization reasons its best to apply tool texture "nodraw" to areas that will be rendered but never be seen by the player.
Here is a great guide on optimizing your maps and probably find more info to your questions. Good luck.
http://www.optimization.interlopers.net