I had to look around. It appears that the standard method for providing backlash is in tooth profile (JIS, ISO, etc.). It seems as though you have nothing to worry about as it should be built into the gears. If you were making gears you'd have to be sure to cut them accordingly. The KHK site calls out backlash for every gear. I worked at a place that custom made every gear they needed and they were always modifying profile to make their gear ratios fit and reduce undercut on small gears. Sorry to make you worry about nothing.
When the situation allows, doing like Jason suggests is certainly applicable.
Greg