CR: the way it's planned right now is to have two batteries in series to go from 3.7V to 7.4V with the same Amp output. Take that voltage and pass it through a regulator that's going to give me a 5V and 3V3 rail @ 2A each (this from Linear). When the batteries need to be recharged, there will be a 12V DC input that will both recharge the batteries, as well as feeding the regulator (so the device continues to run.)
Chagrin: I will never assume that two batteries are identical. Car batteries aren't and will die over time too. By using single cells, at least I can monitor each one separately and keep them close to one another.