I would start by looking at laying them down in rows along the right side, and try to put all the electronics on the motor side. However, your quark is quite big, so space will be tight. I don't know if it would fit where the Th servo goes..
You may be forced to put the Q125 over the shocks (PITA) or stand all the cells up. Standing the cells up will give enough room. I had to do this on mine:
But I also designed my truck to accomodate nimh, lipos and A123s, and retain manual brakes. If you design it just for A123s you may come up w/ something more optimal.