I organize my boxes to particular insect or type - Baetis, PMD's, March Browns,Caddis, Midges, Streamers and Buggers, Attractors, Stoneflies and a lot more:
Baetis/BWO's
Attractors/Euro Nymphs
MIDGES
Sparkle Pupa - deep and emerging
Buggers and Streamers
Dries and emergers for most Caddis and May flys have their own compartment boxes...
PT/TB