I remember struggling to keep a single fly box stocked as a kid. I wasn't tying yet and flies were expensive. Every one counted. After 10 years of guiding, I've run into the opposite problem. I have so many flies and boxes, organizing them has become an issue.
As a guide, I carried a boat bag with numerous boxes categorized and labeled. I had plenty of time to sort through them and make decisions while the anglers fished.
When I would go wade fishing solo or jump in a buddies boat, I was rarely prepared and would shove a handful of random flies into a box and rush out the door. I just didn't want to carry all my guide gear.
Now that I've come full circle and don't require an army of flies for paying customers, I am working to simplify my approach in a manner that has me prepared with my favorite patterns in a few simple boxes.
I really only use a handful of patterns the majority of the time and figure 3 large boxes in the simple foam style will work for most days. Then I'll have special circumstance boxes for specific situations and species. In order to do this, I am eliminating all the patterns I never use. I have flies that have seen 10 states and a few continents without touching water. Time to cut the fat and put them in a retirement home. Here's the new logic:
Dry Fly Box
Foam bugs and large attractors on the flat foam and parachutes, comparaduns and fragile flies on ridged foam. Lots of simple parachutes, elk hair caddis, stimulators and some technical emergers and cripples. Foam and deer hair dries on the larger end to match stoneflies and terrestrials.
All the weighted big boys on the flat foam, everything else on the right. Lots of girdle bugs, Doug Ouellette's Stonedaddy, princes, pt's, hare's ears, Czech nymphs, scuds, worms and some more specific mayfly imitations for technical situations. Also a few zebra midges and brassies in case I leave the midge box at home.
Midges get their own box since they are so small and easy to lose. Brassies, zebras in a variety of color combos, rs2's, tubing midges, thread midges. Some with beads and some without. Mainly for tailwaters, cold seasons and technical fisheries.
Pack it full of my favorite buggers and articulated flies. Meat and more meat. Some unweighted for fishing on sinking tips and others with cones and weight for fishing on a floater. Home invaders, double bunnies, cheech leeches, etc. A wide range of color combos to fit different lighting situations.
Damsels, Dragons and Chironomids get one large foam box for stillwaters. This includes mohair leeches, small buggers and lake specific streamer/nymph flies. They are typically fished on a retrieve anyways.
Mainly Damsels and Dragonflies in a large foam box. Also a few hoppers, beetles and ants. The standard dry fly box will cover everything else.
All the swinging flies, skaters and nymphs for steelhead and salmon in a single large foam box. I could do 2 boxes but I live in Montana and only do a few trips each year.
A single tupperware container to hold 15-20 large pike flies. They are hard to lose so no reason to even use a foam box. A ziploc bag might even be a better choice. I keep a spool of wire bite tippet in this container as well.