I have two large divided boxes (10"x7") that have 17 compartments each (1 large, 16 normal) that I separate all of my flies into (type and color - but you could get more and go with size as well). I carry just a few small fly boxes and every so often (usually about 4-6 times out) I empty my fly boxes back into the the large boxes (and throw out the flies that are too damaged to reuse).
Whne I go fishing I make sure I look through my fly boxes to makes sure I have at least 2 of evey kind that I think I will need and by looking at the large boxes first I can make sure that I have thought of everything.
Sometimes I take the large boxes with me in case there is a fly I need to have, once I'm on the water. But this past year I have even broke myself of that. If I don't have it in my small box, too bad....
It works for me because the fish I chase have simple requirements. Tailwater fisheries would require larger carry boxes, but the idea could still work: 1) Organize and categorize your flies into a large collection and 2) only take the flies you need. 3) From time to time empty your carry fly boxes back into the larger collection and start over.
I even took it a step farther to capture the flies I need to always tie and have on hand:
Anal, I know, but I'm able to stay organized...
"Even a fish wouldn't get into trouble if he kept his mouth shut."