a gravel vac or siphon can be used to hoover the crud off sand, simply hover the vack just above the sand so it sucks the crap up but leaves the and behind, you also need to remember to stir your sand as anareobic layers build up as things decay in the sand, and this may become harmfull to fish.
and yes guppies are great sand is in most cases better for plants as they anchor better in it and especialy if you use root tabs or such like then they thrive much like my tank