Hi Mark,
The 6V/12V jumper inside the V2 is for setting the auto-shutoff and low battery indicator. This was necessary for sealed lead acid type batteries where their voltage would slowly drop as they became discharged. The battery you are considering is a Lithium Polymer type that has a regulated voltage output and built in low battery indicator/auto-shutoff, so there is no need to adjust the voltage settings inside the V2. A 6V V2 will run with any voltage from 6-15V without a problem. The only caveat with running higher voltages is that the battery won't last as long and the unit will run slightly warmer, nothing to be worried about.
I would suggest using a 6V battery if you can since it will run longer, but if you want to use that 12V battery you can do so without worrying about changing the settings inside the V2.
Please let me know if you have any questions!
Take care,
Alex Vallejo
Grace Design Customer Support