I only carry one box
One of those large inexpensive, flat foamed, fly shop logo ones
I 'feed it' out of a bunch of the Plano style boxes that I carry in my tackle bag
You can make a suitable box by gluing craft foam into an old VCR box
Flies that are too large for a fly box, go in zip-lock bags
Be sure and write you name and phone number on your fly box just in case
The simpler the outfit, the more skill it takes to manage it, and the more pleasure one gets in his achievements.
--- Horace Kephart