Yes that is why you would stir sand or gravel for that matter, it is so anaerobic pockets that can become exposed do not do so.. this biological filtration method is for making a place to cultivate and protect the anaerobic bacteria.. It is much like the DSB
method wich there is a SW
monster island thread devoted to the subject.
This technique isnt new.. there is alot written about the subject.. here is a google search
on "Dr. Jean Jaubert Live Sand Biological Filtration plenum" very specific to try to limit the results some..