I have two different stashes; one for the boat, and one for home storeage of back-ups / refills.
For the boat, I use 3700 and 3600 size boxes and sort by style / type, and then color. I use the bigger boxes for worms, lizards, jig trailers, etc. The smaller boxes hold my senkos, tubes, drop shot baits, craws, grubs, and smaller sized baits.
By using specific boxes for different styles of baits, I can limit what goes in the boat, reducing clutter and weight. I just grab what I need. For example, my 10" worm box only gets used in the warmer months on structure, so it stays in the garage until May.
For the extra / refill plastics at home, I bought two of the largest sized Plano plastic boxes available (roughly 2 1/2 x 2 1/2 and approz 12" thick). these have no dividers in them. Then I grouped the baitys by style, leaving them in their bags, and put them in 1 gallon freezer bags (i.e. jig trailers, craws, 10" worms, etc.). I use a Sharpie to label each freezer bag.
One of the big boxes contains worms, senkos, lizards, trick worms, flukes, etc. The other big box is stuffed with trailers, craws, tubes, etc.
When my boat supply runs down, I go to the big boxes and refill out of the back-up. Freezer bags have really helped me to get and stay organized.
Each winter, I will take an inventory and refill the home stash to make sure I have enough for the year.
This works well for me.