I'm not sure what puffers would prefer, if any, but Sand is a great medium!
As for Vacs, if you do this 2x a week you can get away with "hovering" the vac just over the sunstrate, but every 4-5 weeks I would gently press the Vac about 3/4 to a inch down and gently raise to allow the sand particles to rest out. You will pick up some sand, but it very little in the scope of things.
Also, a periodic "stir" is a good suggestion for sand as well to open an aerobic pockets. I do mine every 4 months or so, but others may suggest different (I'm new to sand myself for the past year)