Having 12 cells wired in series is the same thing as having one battery pack that has 12 cells in it. You can have two 6 cell packs and to wire them in series you take the negative of one pack into the other packs positive, then you wire the extra wire on each pack ( a positive and a negative) to your connector for the speed conroller and voila! you now have the same thing as one big 12 cell pack. It gives you more volts with the same amps.

If you wire them in parallel, it give you the same voltage but twice the amps, (easier to fry expensive controllers)

Hope this helps