Something I've been in the habit of doing when float fishing in a canoe is to take a length of chord small enough to pass through the eye hole on my fly boxes and tie a knot in the end of the chord, then thread the boxes on. Next I tie the chord to the canoe above the boxes. I take the other end throw a slip loop around the butt of the rod below the reel then tie the end of the chord the the handle of the rod above the reel. When I'm fishing, I can slip the rod off the chord easly enough and tie it back on when going from place to place but my fly boxes always stay tied to the boat. You can also cast with the chord tied to the rod and it doesn't get in the way too very much, but you do have to mind your line so the two don't get tangled.
Hope that helps.
Terry