I asked a very similar question here -
http://www.pg-hq.com/comms/showthread.ph...68#pid1368 - to which Vice answered.
I started organizing my units by nations except for KSF, as I would like to keep my die-cut counters separate from my laser-cut counters.
I also started looking at pill box for leaders. I am thinking of using 1 box per two-nation game. 2 nations x (1 compartment for Lt + 1 for Cpt + 1 for others) + 1 compartment for aircrafts and other game specific marker.