You definitely do want to watch out for covering up live rock with sand -- I made that mistake when I had some live rock rubble in a skimming chamber and added sand to it to create a deep sand bed in that area.
I dumped the sand over the rock, and everything was fine until I decided to take the rock out. It was only a few weeks or a month later, but when I did I noticed a really bad smell, turned off the pumps, and checked for ammonia -- sure enough, some was there.
I had covered up some animals, which died and rotted in the sand bed, and then let it all out by stirring it up.
You can always just use some pvc pieces as a base to lift the live rock above the sand. Some people like to do this to allow water to flow underneath so detritus does not accumulate against the rock.