Ok, hoping this helps as i have all my tanks with a sand substrate (play sand!)
This is how i do my tank cleans/water changes.
1/ Clean off anything on tank glass, using magnet, scraper and scouring pad if necessary.
2/Siphon out using just the tubing mentioned before, hovering just over the sand (if you use a gravel vac thing you'll find the end peice is so wide the poo will sink again instead of going up the pipe as you cant bury the end in the substrate as you would with gravel, so dont get one of those).
I take out a couple of buckets of water, then...
3/ With the wrong end of a net or whatevers handy (planter, scraper handle), i dig about in the sand to loosen it up. If you havent done this before, ONLY do a small section of your tank or the amount of toxic gasses you release could kill your fish. Next time do a different bit.
I also move one item that is sitting on the sand and either hoover under it or net out the cr*p and dig the sand up under it. I do one item in the tank each time again to avoid releasing excess waste.
4/ Finally remove another half to one bucket as youve just stirred up a load more muck.
5/ Net out any dead leaves, large bits of poo missed etc - sometimes i drag the net through the sand to catch anything ive missed as the sand will drop through the net and the poo wont.
If you need to give your filter media a rinse do that at stage four in teh last bucket of water, never in tap water.
6/ Top up with your clean conditioned water and have a final check for dead leaves etc with the net.
Done
Em