i have found it is easier to put all of the baits/tackle in 1 or 2 double sided tackle boxes so they are right there and easy to use.

Good idea, but wont all the hooks get tangled from flipping it over, if you are storing crankbaits or other baits with treble hooks?

Uh, huh? I wouldn't even begin to fit a tourney load in one or two boxes. I mean... there are times that I have six crank rods on the deck with three colors of the same crank, in rattle and non-rattle versions. There's one box. Take that in three or four sizes and you're already over your suggestion, and that's for one color of crank.