I also put my brigades in order from veteran to rookie within each division. IE my most veteran units are 1st Texas, 1st Arkansas, 1st Tennessee, while the greener brigades are 5th Texas, 5th Arkansas, 5th Tennessee. I know it sounds a little silly, but it really helps me control the battle at a glance. Each division has a good mix of elite units and rookies, so when I'm ordering around whole divisions, they're fairly diverse.
To make it even more interesting, each of my corps represents a region. "The Southwest Corps", "The Southeastern Corps", and "The Atlantic Coast Corps". That way, I can look at a brigade, say the 1st Arkansas, and instantly know its level of experience, which division it belongs to, and which corps it belongs to. All without loosing the feel of the game by giving each brigade a number code. Not that there's anything wrong with the number code thing, but it's not really my style.