edward 2, you are opening a whole can of worms on this one...
There are MANY ways to get to 12volts, but some make more sense than others.
There should be some specs on your dyno which would include voltage and amperage or wattage. If it is indeed 12 volts, there is no advantage to using two 6volt batteries over one 12volt as long as it has the necesarry amperage.
If you can find any info on the dyno, post what is ays and we can help you out with recomendations.
To find amperage if your spec is listed in wattage, divide wattage by voltage.