Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
If you think there really is a problem with the sand, and you want to stir it without disrupting the plants use a stick, like a chopstick, or shish-kabob skewer and poke the sand with very little stirring action.
If you see a lot of bubbles STOP. You might have some anaerobic pockets that are the home of bacteria that produce some pretty bad gas that could kill the fish. Do a water change. The next day poke a different area, until you run into another pocket of gas, and do a water change. Keep that up, it might take a week to get over the whole tank, then it is time to go back and do the first spot again.
If you can, remove some of the sand over the worst spots so there can be better water circulation in those areas, under the substrate.