Depending on the size of your tank there are different sized gravel vacs.  This usually gives you a nice ratio of speed that it sucks out to how much water you have.  If you buy a really big gravel vac but have a small tank it will not work very well.  To use a gravel vac you can lower the tube to just above the gravel to suck material off the top.  What you do next depends on the size of your gravel and the speed the vac sucks out.  When you press the tube down into the gravel it will begin to suck the debris that has collected in the gravel out up the tube.  It could be possible if the suction is too strong that it would suck the gravel up the tube with it.  In most cases it will flow about 1/3 to 1/2 of the way up the tube and churn around letting the gunk flow up the tube while the gravel starts to fall back into the tank.  You press it in and let it suck for a second or two while you start to lift it back up and move it over to a new spot.  Every couple plunges you need to let the gravel fall out of the tube or it will eventually stack the gravel up to the point that you end up suctioning it out.