one battery is in what i think is the stock position. mounted in a box horizontally in the starboard locker pushed up against the backrest wall. the other battery is in a battery box in the port locker in basically the same position as the first. its horizontal and pushed up against the back of the backrest wall. since the port locker is continuous with the port underseat storage, it can be pushed up a few inches further toward the bow. what i have noticed is that the ballast bags just push them forward and form around them. neither is in danger of being pushed over and the compression of the battery boxes may leave the lid a little crooked but it stays completely covered.
my 1, 2, 1+2 switch and my 180amp fuse are mounted on the inner wall just next to my battery in the starboard compartment. i mounted my dual bank charger in the same spot in the port locker. all the wires run across the tranny in one huge zip tied bundle. i put sleeves on the wires where i was worried about any chafing.
hope this helps.