If you have room in your boat (one extra storage box), what I did is get a two plastic tubs - the width of a ziploc storage bag. I leave all of my plastics in the original bags - unless bulk. And place /organize each style (worms, lizzards, brush hogs, etc) in a large ziploc storage (freezer are a little thicker, and I use the standard bag and not the zips). I can arrange these full bags in the tubs- like a file cabinet. I take a peice of duct tape and make a tab/tag on the top and label it, I can see from looking at the top, and pull that bag out. I fish, mainly with plastics, so I use a bunch - and this has saved a bunch of time on the water, and easy to prepare for a trip.

But I think it takes up less space to keep them in the bag, and organize them into bags than to place them in boxes - and a lot less hassle too.