Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
If you want to vacuum that substrate deeper, be careful. It is very light, and will get sucked up into the vacuum quite easily.
I only vacuum it if I am moving the tank, tearing it down.
Most of the time I do as Calmoa suggests: Keep the vacuum away from the substrate so the substrate does not move, and just get close enough to the plants to remove the obvious debris. If you are touching the plants with the vacuum, and the leaves are not in danger, that is OK. Otherwise brush through the plants with your fingers to dislodge the debris, and vacuum it from a distance.
Another way is to make the flow slower, usually by pinching the outflowing water tube.