You do want to put the "dead" sand on the bottom and put the live stuff on top. I know some who will drain their tank almost completely and just add whole sections of the original sand bed as is. Never heard of the whole die off from under the top layer. My 6" bed always had life in the bed no matter the depth. The gases were stirred up when moved, but that wasn't a promble when adding it to a new tank, just when the live stock was in the original tank is when that can be a problem.