I have a duffel bag, non-military type with a zipper in the side, that everything goes in if its a flying trip. It will hold waders, boots, fins, float tube, rods, everything.

For my normal fishing in the area, fly boxes stay in the Fishcat, waders, boots, pfd, lanyard, rain jacket, etc, goes in a 30 liter dry bag that fits behind the seat of my Fishcat. I try to remember plastic bags to put wet boots, waders in at the end of the trip. I added the bottom inch or so of a 5 gallon bucket to the bottom the dry bag after it started to leak a little, it fit almost perfectly.