Personally, I'd vacuum out all the CC I could reach in 1/2 the tank, and put the new sand on that side. In about a month, I'd do the same to the other 1/2. That way, some critters residing in the CC get a chance to migrate to the new sand. Plus, I wouldn't be all that anal about getting all the CC out from beneath the rocks - get what you can, whatever is left will provide some variability to the substrate (IMO, a good thing).
Kevin
Kevin