I ran my rock in a barebottomed tank for a few weeks, running my big skimmer on it the whole time. put some powerheads in there too, as much flow as you can. Scrub the crap out of it with a hard plastic bristle brush often, and when the crap has settled to the bottom of the tank, siphon it out. when you're confident that there's hardly anymore crap coming off of the rock, give it another week then move it to your tank.
When i finally moved all my rock into my display, i had coralline algae growing on the sides and bottom of my rock tank.. it was almost a month.