I don't use a jig much but, I think I use a unique storage/organization method. Here it goes:
As a co-angler I use speed binders for my spinnerbaits and jigs. This way can account for carrying them both, and keeping them organized and only sacrifice the space of 1 3700 box. (2 speed binders are the same size as 1 3700 box)
I found keeping them in their original packaging when I separate them into their bags in the binder helps keep the baits integrity.
It is also a good way quickly reorganize if I am going to a lake or river where I will need more fb-heads or flippin jigs.
I don't put the jigs/spinners back in the bag until they are dry to prevent rust. And if you use a speed binder for your spinnerbaits don't overjam your tackle bag or storage boxes. The wires/blades will get bent to hell. Other than that I found it to be a good system for fishing out of someone else's boat.