Batteries: Two-6V In Series, or Two-12V In Parallel ???

Costco is a good source of the 6 volt deep cycle golf cart batteries in the west, not sure about the midwest. You could also look for an Interstate Battery dealer or a golf cart dealer. The 12 volt batteries you've been using are probably not true deep cycle batteries so you should see better longevity when you change to true deep cycle batteries. If the battery says something on it like "Marine Deep Cycle" then its not a real deep cycle battery.