I am organized similar to Maurice. I carry 4 fly boxes with me at all times. Two boxes are swing leaf, so essentially it’s like carrying six fly boxes. I took count, and I found that I carry 1000 +/- flies with me at all times. The truth is I probably only fish with less than a dozen different patterns 80% of the time! My boxes are organized in this way:
Two boxes for dry flies. Note: ripple foam is best for dry flies because it allows more room for the hackle without crushing it. Of the two boxes, one has mayfly dries only. The flies in the box are organized by species – BWOs, Hendricksons, Sulphers, etc. One area has attractors.
The second box has all caddis and stonefly dries separated by species.
The third box has all wet flies, nymphs, etc. Flat foam is okay for them, you can pack more in flies in since you are not worried about crushing the hackle. One side has MF nymphs / next side emergers and wets / midges / junk flies (SJ worms, green weenies, egg flies, etc.)
The next box has caddis larva & pupa / stonefly nymphs / terrestrials / streamers & buggers.
My suggestion for you just starting out is to have use two or three fly boxes, depending on how many flies you have:
1st box – All dry flies – separate by mayfly caddis, stonefly, attractor, terrestrial (ripple / ripple foam)
2nd box – All nymphs / wets / pupa - separate by mayfly caddis, stonefly, junk/attractors (flat / flat foam)
3rd box – Streamers / buggers etc. – (flat / flat foam).. They take up the most room. You can eliminate the third box and put your streamers and buggers with your nymphs and wets.
With this set up, when you’re on the stream, and want to fish on top, all you dry flies, separated by type, are in front of you in one box. When you want to fish below the surface, all your nymphs and wet flies are together one box.
I don’t believe you need more than the $10 plastic fly boxes with foam. The C&F slit foam waterproof boxes are great, but I can’t see spending $40 for a fly box.
Two useful tips:
I put a label on the top of each box to ID it when it’s sitting in the pocket of my vest – Dry MF, Dry Caddis/ Stone, etc. With one glance I can easily pick the fly box I need.
I attach some heavy duty Velcro loop section on the bottom of my fly boxes. I attach the hook part of the Velcro to the end of some old of fly line 12” long (you can use an old shoe string or anything). I attach a safety pin to the other end of the fly line and pin it to the bottom of the pocket of my vest. When (not if) you drop your fly box while you're on the stream, it is attached in your vest pocket and it stays with you. With the Velcro you can remove the box from the vest when you need to, and reattach it when you’re fishing. It works well for me. I lost more boxes of flies than I care to remember before I began securing them to my vest pocket. Good luck