I have 12 volt gel batteries in my boats so hope it is OK to keep on their sides
Keep them as low as you can get them, and on the centre line of the hull as well, this will help as ballast and lower the center of gravity, Nothing like watching your pride and joy capsize because its to top heavy
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I don't worry about a box I strap my batteries in with some cut down lugage ties I picked up from a local cheepy shop. I think poundland do something similar as well, they don't move and if you want to take battery out for charging its just undoing a couple of clips, (this way is also usefull if you want to experiment with other batteries as the straps are adjustable