If you want to go deeper than just barely at the surface, here is how I vacuum sand:
1) Hold the intake at an angle that allows some water from above the surface to enter, and only half or so of the intake is actually into the substrate.
2) Drag the vacuum through the substrate, do not push it. Otherwise more substrate will get pushed up into the intake. Or else lift it up and down as you move from spot to spot.
3) Hold the outlet tube in your hand, ready to pinch it off to slow or stop the water flow. This will release substrate that has been building up in the intake tube.
Remember that as the plants root and spread you will not be vacuuming where their roots are, so that you might just end up vacuuming a very small area of the substrate. Mostly you will be getting close to the surface without actually touching the substrate.