1. We have airstones with our sand and the fish sometimes pile the sand up on top of it, but so far we've had no problems with it clogging up or anything. We just take it all off when its time for a water change.
2. You just hover the vac an inch or so above the sand and it will suck up all the nasty stuff, not the sand. Unless its a real light-weight sand you dont have have to worry about it
3. As long as the sandbed is deep enough you shouldnt have any problems unless the fish you have like to dig them up
