To save air space, you could try jig or tackle pouches, although ziplok bags would be a cheap experiment.
I currently organize all of mine in Plano 3600-style boxes, which it sounds like you are doing. I did have the boxes in a tackle bag, although I just rearranged the boat so that I didn't need the bag and now store my tackle in the built-in storage compartments. Typically, my most used ones get combined in one or two 3600s while the ones I haven't touched in a while get combined into archive 3600 boxes which might not be in the boat all the time, since I'm also hauling crankbaits and other long line setup tackle as well. I'm also rethinking my supply and extra stashes to possibly keep plastic jig supplies in bags again.
If I'm not at work or taking kids to their activities, you might find me on "The Rez" fishing. If not there, I could be in the garage working on my boat.