Mine are all organized in different boxes like this:
Shap raps (I know these just from looking at them)
Squarebills
Shallow (1-6 feet)
Mid (7-12 feet)
Deep (13+ feet)
Walleye/Trolling
Some of my deep divers may run 14 feet, some of them may run 22 feet. Most of them I know what they run, but if I don't, I can usually figure it out just by the bill and weight of the lure. If if that doesn't work, it doesn't take long to throw something and see if its hitting the bottom or not in whatever depth I'm in.