if you stick it directly in the substrate, the gravel vac will suck the sand right up. but on the other hand, any waste and debris that isnt taken care of by the pleco is whisked away toward the center of the tank by the powerheads (when they're working

) and i have gravel in the center, so its easy to vaccum up.
if there is any debris on the sand, it will be sitting on the surface and take a fairly long time to break down. in the meantime, i hold the end of the gravel vac about an inch away from the sand and it will suck up the debris and leave the sand pretty much intact and undisturbed. it's really very easy to take care of. and if you're interested in raising clown loaches, they love the sand.
to be honest, my sand is just from a cheap bag of sand that i got from Home Depot. i rinsed it out the best i could, and it hasnt brought in any harmful substances or organisms since i've had it for the past 4-5 years, so it did okay.
*edit*
and when i change the water, move plants around, or do anyhting that will kick up the sand, i turn off the outside filter (an Emperor 280). but under normal tank operation, the sand stays settled and won't cause any problems with the filter.