If you wire them parallel you get double the mah which gives longer run time, longer run time. The right pinion depends on a few things, testing while monitoring the temp is the best thing to do.
If you wire them in series you double the voltage and burn it up regardless of the pinion.
A little side note, my MERV came with the speed pinion installed, contrary to the owners manual. As Smaxxin mentioned, you really need to monitor your temps to get your gearing dialed in for where you will normally run the truck. I ended up running the optional pinion and I think a 52T spur as well for where I run, and I run 2s batteries almost always.