I have an amazing mismatch of flies from various shops, my own ties, trades, etc. I do group them in the Richardson. I don't separate by tier, but I do separate by type of pattern.
Deep tray (closest to chest) - Big flies on bottom (streamers, big stoneflies, etc.). On lid, half of it is egg patterns, and the other half random attractors. Also, terrestrials.
Middle tray - bottom is all "exact match" dry fly patterns. Grouped by species, and by tie. For instance, in sulphers, there's cut wing thorax's, then parachutes, then comparaduns, then spinners. The lid is assorted PT nymphs on the left. And mostly "small flies" on the right, which includes the very small BWO's, midges, tricos, etc., in all life forms. I have 10-15 parachute Adams' also on the lid.
Outside tray - caddis (all stages). Also scuds, shrimp, and Hare's Ear nymphs.