I keep Plano 3600 and 3700 boxes stocked with my most often used stuff. I keep them in there original bags in a tote and refill the boxes as needed. I have used 2000 different systems over the years, and this is the one that stuck for a couple reasons:
#1 no digging around for bags, or having empty bags all over the boat. A quick look at the box, and I know what is in that box, and when that box needs to be refilled.
#2 It keeps the baits "straighter", and if I do get a bag with some bent up baits, an afternoon on the boat deck, in the sun, softens them up and makes them "straight" again.