Andy
I've got a cut off switch on the negative of battery 1 (under air box). It's a terminal mounted switch which I have added as a temp measure until I get round to fitting an switch which it easier to access. From the drivers seat I can "just" reach between the air filter and the battery box to reach the switch, with the lid removed.
See below:
http://www.ebay.co.uk/itm/Battery-Disconnect-Switch-Isolator-Cut-Off-Switch-/360484845730?pt=UK_CarsParts_Vehicles_CarParts_SM&hash=item53ee9238a2
Works a treat, but not if I need to cut the batteries off in a hurry!! (if you know what I mean)
Good for security too.
Cheers
Matt
P.S. if you batteries have been flattened beyond a certain point, they won't recover i'm afraid. Once a lead acid battery drops below a certain voltage it will never return to the same capacity.