I'd guess both the boat battery case and a bungie would work. I think both would hold the batteries "in place".. By bungies, I'd guess you are referring to the real heavy duty ones you see truckers use to hold their tarps in place. Common rubber band bungies such as those found in hardware stores with the cloth covering would be pretty useless, I'd guess.
If you plan on sticking with the single 12v battery, I'd probably want to go to the local Kragen/Checkers or Pep Boys.. or whatever auto parts stores you have and pick up a real battery hold down. It would mean drilling two holes in the pan of the battery box and running the "L" or "J" bolts up to secure the hold down in place. The bolts would probably need to have some sort of caulking placed around them where they go thru the pan so they don't fall to the ground when you take off the hold down.. but, that'd be only once every5 plus years.. so, wouldn't be a real inconvenience.
Coaches ride pretty smoothly, especially toward the centers where most batteries are held.. so, other than keeping them from shifting, I wouldn't expect the batteries to suffer from physical shock damage.
Good luck.. I'm sticking with 6 volt batts.. unless I decide to take my son up on providing me with a lifetime supply of 4D batteries..