I'm with many of the others here. As long as the system makes sense to you, color code any way you want. I personally have three different types and colors of boxes, and typically use one of each per cartridge (so far I only load 6 different cartridges...more to follow!)
I normally reserve the boxes for "working up loads": I wrote series of letters on rows and numbers on columns so that I can combine several different charge weights in one box, and use a simple piece of paper taped to the inside of the lid to ensure that I recall which charge corresponds with which column.
For other "don't matter as much" lots, I'll either use used federal cartridge carriers (with the belt loops on the ends....does anyone really use those things on a belt?) with the load data taped to the back. for high volume, single-data lots, a sturdy ziploc normally gets the nod, with the load data written on the bag.