Your primary source of circulation should be your main pump and over flows, followed by any internal power heads, like Vortechs or Tunze. You need to design your rock around how you want your water to move, the goal typically being to reduce or eliminate dead spots but still allowing for quiet zones for those animals that cannot tolerate high water movement.
So there are aesthetic values, and maintenance issue to be considered while you are laying out your rock and water movements: how easy or hard is it to get to the power heads, the glass, etc..
As for cleaning the substrate, that is typically handled by animals, hermits, snails, starfish, etc...i am not a fan of vacuuming of sand beds...
