Substrate cleaning is an interesting topic and I hope we get a few responses. I have one tank with fine sand (an accidental purchase when I performed my once every two year - or so - bottom substrate removal) and many people prefer it but it does disrupt more easily than something with larger gain. In the one tank I have, it appears that debris stays on top rather than settling in so I am leaving it for now to see if it helps reduce nitrate build up (the reason I replace it at over time).
Since I only have the one tank I can't vouch for my method but this is what I do. During my weekly tank cleaning, I gently siphon the top layer to remove visible debris and then disrupt it along the glass sides (and any place I see discoloration) with my hand, keeping the siphon close to my disruption point. It does not take too long to settle back down but it does cloud the tank.