Many soft plastic baits come equipped with appendages that perform best when stored in original clamshell packaging - swimbaits or flapping trailers come to mind. Clamshells reduce warping/kinking caused by memory, a common problem when baits are packed together loose in a bag or tackle tray.
Ryan DeChaine shares his method for storing bulky clamshell packs in boat compartments. Just about any bag can work, but DeChaine prefers soft-sided tackle bags that expand in a rectangular shape. This bag style conforms to available space, compresses or expands based on contents, and keeps baits organized by size, shape and color. It also removes any guesswork when it comes time to re-order shortages.