The original battery setup was two group 24 or 27 batteries in the narrow spot between the icebox and the engine (more or less directly below the red main battery switch location). This is a tough spot to work, either hooking up the battery leads or checking the electrolyte (assuming lead-acid batteries). If you are starting fresh, I would suggest under the cabin sole is the best location. I glassed in a shelf there, just aft of where the shower sump is, and have three GP 24 deep discharge batteries there - my house bank. I left one GP 27 as a 'starter battery' in the old location by the icebox. Normally I use the house bank for starting too. The starter battery is my back up.
Several owners have put 6 volt golf cart batteries under the cabin sole - its deep enough for them down there. This might be one of the best options. As well, many have replaced the red battery switch (off-1-both-2) with separate switches for each bank and maybe an emergency 'combiner' switch. Maine Sail has written some good posts about battery switching options, both here and on his web site.
Here is a link to one of the longer threads for your reading enjoyment.