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