If the gravel is getting very soiled, there is a possibility that you may be feeding them too much. They really should have no problem getting left over bits and pieces from between the pieces of gravel unless your gravel is excessively big pieces, then they may not be able to reach them.
When you do your gravel vac, place the big end of the tube directly onto the gravel, this will pick up the much and a little of the gravel will lift into it, but this should drop back out as you move the tube.
If you're very worried about your guppies being sucked up (they shouldn't tho') try putting a torch at the other end of the tank, I've found (with fry) that they will either head toward the light or away from it (depending on the fry!) that way you can vac in peace and move the light as you change ends.