1: I have a wall protecting my fort, and 3 levels up I have a small roof covering the walls below it, If I place a seige engine on top of the roof, will they target enemies in front of them but 3 levels down?
2: If a stray stone is launched and lands on a road, will it destroy the road?
I'm not sure, but I don't think ammo will harm a road. Ammo from siege engines travels 'till either they crash to the ground as determined by the the siege operators skill, or they hit a wall and there is empty space below it. Then it is turned into the item(A boulder will turn into a regular stone, like when you mine). Falling things other than cave-ins will not hurt anything.
And if you try to get lucky with a falling shot, don't bother. Any projectile that falls one or more z-levels will become an inert item that won't hurt anything and won't be destroyed normally.