I use only AA and AAAs and keep them in some old small .. wallets. I take new batteries from the left, put the newly charged from the right side.. and those that need charging, not more than 1-2 at a time, I just put directly into my charger.
check out the pelican case setup thread in general flashlight discussion. Tons of great ideas for case setups for lights and batteries. I personally use a small peli case with pick and pluck foam for all my AA, AAA, 16340, 14500, and 18650.