I organize by size but in two seperate boxes.. One with dries and nyphms, the other with streamers and poppers. Been thinking about putting together a "go-to" box with a mix of everything, but then in my mind, there'll always be that one I'm missing
Basically- newly tied flies, flies that have worked, and flies that didn't work and will be be stripped for hook recycle. Further separation by size as in larger, not so big, and tiny.
On the water a single box may contain all of these but the recyclers, those remain on the drying patch til end of session.
For my still water kayak big bow hunting, I have an MFC boat box that’s mostly chironomids but also dragons, damsels, shrimp, back swimmers, misc nymphs, and leeches. Ran out of room so bloodworms and dries each get their own box. Another large double sided box for boobies and blobs.
For flats trips I have a box each for tarpon, permit, and bones, I gave up trying to keep them sorted by country.