Some will tell you to vacuum the sandbed, personally I think it to be one of the worst things you can do. If you want to remove excess pollutants, fan the top of the sandbed gentley before the water change so the detritus works it's way back into the water column. This allows you to remove some via the water change, your skimmer/filtration equip a second chance at removal and it will feed some corals if any. If there is an abundance, you should also look at cutting back on the amount and frequencey of your feedings as well as possibley bolstering your clean up crew.
In short, just siphon out the water.