We started off with a lot of rock too. The trick is to buy frags, small pieces of corals either free standing or attached to small plugs. You then can glue (using reef safe glue) the coral or frag plug onto your existing live rock. After awhile the coral will grow/attach itself to the rock.
All of the larger corals in my tank (2 years ago) started off as small frags, mostly from other canreef members for good prices. Check out my signature links for pictures. FYI frag plugs are much easier to attach then free standing corals, and yes with time the coral will over grow the ugly plug
*Edit added info.
We use a turkey baster to blow detritus off the rock and off of the bottom of our BB tank. Our sand sifting goby keeps our sand bed clean (in our other tank) and our skimmer does the rest.