If this is for WWII you can try marking the backs of the bases. I've used Roman numerals for squad designation and color variations on those numerals for platoon designation. So platoon one would have squads I, II, and III in white while platoon two would have I, II, and III squads in blue.
Honestly though, since most squads are separated by a few inches on the battlefield I don't really bother with it anymore and just make sure they all have the right number of miniatures to start.
Former Director of Product Development, Research and Design