You're talking about a deep cleaning? Is this a planted tank? If it's not planted, then go light on the substrate, you'll still get all the aesthetic benefits of the nice, dark sand but without seeing the crap that's made it into the deeper layers, or without much in the way of deeper layers.
If it's planted, then don't worry about the deeper stuff, it's just ferts.
The nice thing about sand is that usually stuff doesn't sink into the sub-substrate, but stays near the top since the sand is so fine that it packs together and keeps bigger stuff near the top for the vacuum and filter.
Now if you do need to get into the deeper layers, holding your gravel vac at about a 45 degree angle will help keep the sand from being sucked out. Also the use of a narrower gravel vac (less sucking power) will also cut down on this, but at the cost of increased cleaning time and decreased lifting power. Finally, you can try placing a new nylon pantyhose over the intake, this should help keep the sand out, but it would (I imagine) keep the gunk out too.
How fine is this sand? I use #2 pool filter sand in my 18g tank, I don't have much trouble with getting good and deep if I want to without sucking a tankload of substrata out as well.