Rather than build a two story structure, build a single story one and a smaller single-story building that fits just inside the larger's walls. That way you have the option of playing them as two buildings, or of stacking the smaller one on top of the larger for a two-story. You can put a ladder going to the door of the upper building, or just imagine that it is an extra-large window. It is easy to get involved with complex rules for fighting and moving within buildings. Generally, simpler is better, but different scenarios will have different requirements.
All shots taken within a single building are at close-range regardless of measured range.
How much a building aids defense will vary with the scope of the game. For a game with many figures, attacking troops can just move to the building and melee the defenders normally, albeit with a combat bonus for the defenders. Faster is better than slower. Doing it the same way as something else is better than doing it differently from anything else. Heavily favoring the defender is more realistic, but leads to a longer, duller game than mildly favoring the defender.