I have found that the most effective way of cleaning sand (IMO), is to use a manual siphon to litterally suck out the substrate, and have a large bucket for it to flow into. Once the bucket is full, I will usually dump out the excess water, then continue until I have removed the majority of the sand. Most of the time, no matter how many times I dump the excess water while doing this, I usually need 2 or 3 buckets to hold all of it. Once I have the sand out, I usually do a visual check to make sure none of my sneaky crustaceans have managed to hitch a ride down the tubes and into the buckets (it's almost as if they have come to recognize my technique, and take advantage of it as a free ticket out!) Once all is clear, I move onto the actuall cleaning. Typically on my lazy days, I will use water from the hose or tub to rinse, though this isn't the best idea for saltwater, I know I know, lol. But when I am not as lazy, and have the time and patients, I will usually mix a batch of synthetic sea water, and flush it that way, as this tends to save the beneficial bacteria within. I usually only do this about once every eight to ten weeks. About every two weeks, sometimes more, I simply stir the sand, and use a modified gravel filter/siphon, hovering over the top layer about and inch or so. Either way you choose to do it, it's important reguardless of how, to ocassionaly stir up the substrate. It can collect decaying matter, and gasses that can be dangerous to your livestock if left alone. Having burrowing livestock also helps as they continuously move around the sand. But as a double edged sword, it also makes it worse to a degree, as bits of uneaten food, and waste get shifted to the bottom layers, which is why cycling it is needed. It's really up to you on which method to use, but in the end, it's important none the less.
--EMI