The answer is: it depends.
How much battery do you go through in a day? How often you want to recharge? What 6v batteries you are looking at buying? What 12v batteries are you looking at buying? How much space do you have for the batteries? How much do you want to spend?
My advice is to go online and shop both types of batteries. Look for the best in each and then do the math. Pick the set that works best for you.
Formula for 12v batteries: (AH per battery x # of batteries)/2 = Total AH available
Formula for 6v batteries: (AH per battery x 1/2# of batteries)/2 = Total AH available
Also, consider whether you want to go with AGM batteries for the maintenance free (and non-venting ability) or standard wet cell batteries.