Is there one "best way"?! I'm sure I'll get a mirad of suggestions and opinions, but here it goes...
By bug species (i.e., caddis [pupa, nymph, adult], mayflies, etc.);
By fish species, i.e. bully box, trout box, pike box, etc;
General - dry box, streamer box, nymph box, (or in Don Anderson's case, a suite case of chironomids, ), etc.
or by season, still water, small stream, large stream, etc.
One caveat, of course, it obviously depends on how many flies one actually has, naturally...
Ok... go!!
P