[RyanN]

Originally Posted by Al Skierkiewicz

Ryan,
Unfortunately this is not the case. The six volt battery voltage would rise slightly during the time the 12 volt battery would be able to supply it current. The 12 volt would continue to try and dump current until it fell to 6 volts as well. If both batteries were fully charged to begin with, all the excess current would be turned into heat likely destroying the batteries or at least causing some nasty venting.
In the case of the 12 volt batteries in parallel, one will always be slightly higher voltage than the other. This condition will cause current flow between each of them as they ping pong trying to deliver current to the lower voltage battery. Without diodes directing current flow, the two batteries, over time will deplete each other right down to zero volts.

Brent,
The way you hooked up the power will work until the backup battery falls below the 7 volt cutout on the regulator. At that point the regulator is no longer functioning and acts more like a resistor. It may work for a while but may not be reliable.

Interesting fact I did not know about 2 of the same voltage batteries depleting each other...
And I was pretty sure that there would be some nasty venting if one were to try to parallel 2 different voltage batteries (hence the reason I said not to try this ).
Also, Brent said that he was using the Digital I/O port to supply power, which is a regulated +5V from the main 12V battery. It does not rely on the backup battery.