I've seen them eat some flakes, but they really prefer the shrimp pellets and algae wafers-both of which you can get at most pet stores.
I doubt they stir up the bottom much at all-they have small mouths, and typically orient themselves nearly vertically as they pick through stuff on the bottom. They'll pick up little pebbles in their mouths, roll them about, then spit them out, but don't really stir up large areas, at least in my observations of the juveniles.
