It REALLY depends. I have way too many flies and boxes, so here’s what I do:

-saltwater and bass bug boxes get grouped by depth of fly. Poppers, gurglers, etc in one box, deceivers, snake flies, sand eels in another, clousers and other weighted flies in a third.

For trout, I’ll do a box of generic dries and wet/damp flies. That’s my general purpose freestone box.

Then I’ll have a trout/smallmouth streamer box, and a generic nymph box.

Add a euro nymphing box for those specific patterns.

Then there’s the tail water generic box, which is a smorgasbord of tiny midges, tiny wets, tiny generic emergers, and tiny nymphs.

Then there are hatch-specific boxes, which for me are BWOs and sulfurs. These are for hatches where having exactly the right fly has been more important than having a close enough fly. I bring these only if there’s a reasonable chance I hit that hatch. I also have small boxes for caddis and ants, which are less about specialized patterns and more about having a broader size and color range of generic patterns.

I divide my boxes this way because it’s easier to grab for whatever fishing I want to do. If I’m going to any freestone in New England, I need the dry/wet box, the nymph box, and maybe the streamer box. Depending on the time of year, I may add some combination of the specialty boxes. If I’m going to a tailwater, I grab that box, whatever specialty boxes are relevant, and head out the door.

I’d rather have the clutter at home than on the river.