I mostly fish from a sit-in kayak so a soft sided 3600 box is about all I can fit. I have 3 rod holders so I keep 3 main trays, with just enough room for two halfers- one for random terminal tackle and extras, the other for my UL river/panfish gear.
Tray #1 is heavy cover- mostly frogs, jigs and strange weedless stuff.
Tray #2 is plastics, hooks and weights. Craws, worms, minnows and the stuff to peg them, C-rig, punch weight or shaky head 'em. Plastics are my comfort.
Tray #3 is hard baits, vibrations and moving baits. An assortment of squarebills, jerkbaits, traps, spinners and smaller swimbaits are all lined up together.
I have backups and more at home but the 3 seashells er... Trays system works great to keep it simple and cover most of my bases.