Crushed coral requires a lot more cleaning, as it traps a lot of organics that would otherwise get filtered out. Adding small amounts of a fine aragonite sand over a period of time will help "seal" the substrate. I recommend Aragonite because it has a lot of elements that slowly release into the water, and these elements help to buffer your pH (keep it stable). In order for a sand bed to work properly, it needs to have oxygen in the top layer, and little to no oxygen in the bottom layer. Aerobic bacteria lives in the top layer, and this bacteria converts Nitrites into Nitrates. Anaerobic bacteria lives in the oxygen depleted level of sand, and converts Nitrates into Nitrogen. If you look at a healthy sand bed, you can see bubbles in the upper layer. These bubbles are Nitrogen gas bubbles that will eventually make their way into the water column and dissipate into the atmosphere. Having some kind of sand sifters help to release the bubbles, as well as keeping the top layer of sand loose, making it easier for the Nitrogen bubbles to rise up through the sand. The problem with moving your rocks around is that it disturbs these layers of substrate, and hinders the filtration process. Decaying matter and disrupted bacteria can lead to a build up of Hydrogen Chloride, which is toxic to your tank. Long story short... a deep sand bed is far better than crushed coral if you want it to help with the filtration process. You can build up the sand bed without moving anything in your tank. Just do it slowly and gradually. Small patches over several weeks should be okay. Blast a small patch of the crushed coral to get rid of debris, and gently stir the sand into that patch. Wait several days to let things settle, and then do another small patch elsewhere. It will take time and patience, but it will be worth it in the end.