"You don't lose much sand if you suck up the sand into the larger part of the vacuum and then pinch the hose. By doing this you allow the sand to fall to the bottom while the stuff you want out remains suspended in the tube. When you release your your pinch on the hose all the bad stuff is sucked out. "
Fantastic description of technique. Keep a little flow going so the nasty silt doesn't escape as you drop the sand - there will be lots of bad stuff (hydrogen sulfide, etc) in the cloud. It can take 6 months for the anaerobic and anoxic bacteria to develop in the deeper layers. These are the ones that break Nitrates into Nitrogen gas, which bubbles out. If you keep this in mind when vacumming, with such a set up, I tyicially surface vacuum the whole bed to a half inch deep. Then I section the tank out and every water change, I vacuum about 10% of the sand to the bottom. This is where you have to be careful about that silt cloud - siphon all of it out so it doesn't spread and disperse nutrients or disease organisms. By just doing 10% or so and doing a different area each time, you eliminate a portion of the stored nutrient load while retaining most of the anaerobes that eat Nitrates and allowing the vacuumed areas to recover. Oxygen is actually detrimental to a lot of the organisms that live in O2 depleted areas. Those guys get their oxygen for metabolism from Nitrates - NO3. Bob Goemans wrote a great booklet called "Live Sand Secrets" available online and at many LFS. I've got several reefs going on 10+ years with these techniques and Nitrates are well controlled by the DSB if maintained.