+Sakura
Never stir any subtrate, if you like crushed corals, just siphon frequent and you won't have any problems, people here claims that crush corals loses its effient after awhile, but sand has no value what so ever other than it holds bacteria, anything in your tank holds bacteria, when you have a 3 inch sand bed, only the top surface holds bacteria, the bottem of the sand can develop problems too., like I said before, is your preference, proper maintance does the trick.
your options:
sand, crushcorals, barebottem, choose what you like!