I don't really know, I have gravel in all of my tanks. You may have to try hovering farther away from the sand. One thing you can do is us a piece of aquarium hose and start a siphon that way. This gives you a lot more precision, but isn't very practical in large tanks.
Sounds like you are doing a great job treating your little fishy friends. They should be getting back to normal in no time.
On a side note, make sure you use the meds for the full time they are perscribed. Many people will stop using them after a few days when all seems to be well, only to have a recurrence of ich.