The 2 6volts wired to become 12v become a bigger gas tank in essence than a 12v. That, and like was said already, the 6v batteries are made to be drained repeatedly and won't break down over time like the 12v's do. You don't get any stronger juice out of that setup, just alot bigger fuel tank....I know guys that have 4 6's wired in and can ran lights and furnaces all weekend in the Ak winters and not have to recharge them. Costs a little more up front, but way cheaper and nicer in the long run.
Are you comparing 6 volt deep cycle batteries to 12 volt deep cycle batteries?
I guess something to keep in mind is that voltage is only a measurement of electrical potential.
Battery Ratings..
This might help the whole 6v vs 12 volt thing.
If talking all the same technologys, the size of the battery represents the capacity of the better. Note, I am talking energy capacity, there are normally ratings of amp-hours for a specific amperage (Current*Voltage integrated
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over time gives you energy)
If the 6 volt and the 12 volt are generally the same size, they both have generally the same energy content. Since they have the same energy content, and if we assume they can provide the same amount of power (Current*Voltage), in order to have a reduction in voltage from 12 to 6 you will see an increase in current from I to 2*I.
As compared to the 12 volt battery, the 6 volt battery has the ability to provide twice as much current. Problem is, is that it is a 6 volts, which is not very usable. You put two 6 volts in series to give you 12 volts, you now have a 12 volt system that has twice the energy of the single 12 volt battery.
Have you guys looked at RE (renewable energy) use batteries? I know Trojan makes some very pretty red ones... but dang if they aren't expensive. Probably last a long time too... as they say you get what you pay for, but sometimes you only get a big bill...
Trojan PDF for information... note the comparison of the 6 volt vs. 12 volt for the same weight battery. Close to 2 twice as much, but not exact.