I have a tool box that holds all my fly tying tools and threads and some materials that I take to the monthly TU meeting to demo fly tying. It has plastic puka's (that's Hawaiian for little holes) formed in the top of the lid, just the right size for spools of thread, wire, etc, with clear plastic covers. Inside the main box on the top is a plastic tool tray. The tray has two stowage areas running the length of the tray with a 1/2 or so rib and handle dividing the two areas. I glued a strip of wood in the rib area under the tray running the length of the tray and drilled various size hole in the rib/wood and in the handle/wood too. I then sort whatever tools I need for a particular fly, putting the scissors in the holes in the handle/wood. I use the tray as my tool caddy on my roll top desk at home, that way I don't often leave any tools behind when I take the box with me for fly tying demos or when I go camping/fishing with my son's scout troop. I have one bobbin with 6/0 white thread, one with black 6/0, one with black 8/0, and one with tan 6/0 thread and one extra bobbin that I put other less often used color/weight spools of thread. Works for me!
John