This would be for the way you are asking.
I would prefer this way in my own car.
You probably should upgrade your alternator to something bigger if your running your amp on a 1ohm load, above 1ohm you should be fine until you have the lights, heat and wipers on at the same time, then just turn it down.
You can think of adding a battery this way a 12 volt car battery has 6 2volt cells in it, they are like little batteries stuck together. In example one it is wired to make the cells bigger, so they can store more power, and you can get more amperage. In example two it is like adding 6 more cells, so you get more voltage, 24 volts actually, that is bad in most situations, your alternator won't charge them because it needs to be at a higher voltage than the batteries to charge them (around 13.5 - 15 volts for a 12volt system) and if the batteries are put in with a charge already in them they would most likely blow your lights and kill your ECU.