Instead of organizing your fly boxes by type of fly organize by color. Whatever colors you have the hardest time telling apart keep those flies in different boxes of different tones: one black, one white, a few in various shades of mid-tones grays. You may be color blind, but you should still be able to distinguish between light and dark colors. Don't forget to mark the color of the flies that are in each box on the outside of the box.

My fly fishing partner has the problem, and I fished with him countless times UNTIL one day on the water he said something about the color of a fly he was using, and I said "What?" He said, "Isn't that a (certain color?)" And I said, no, not even close. Then he told me about his color problem. If you are buying flies, I would buy them described by the salesperson, and limit my color variations. You don't need all the different colors. Fish are as color blind as you are..depends on the light present as to how well colors show up to a fish, or how deep the fly is fished...colors disciptate very quickly in depth. Light colors, and dark colors...the shades are more important than the actual colors.