Two 6 volt batteries are not necessarily better than a single 12 volt.
The theory behind using 2 6volt batteries is the fact that you have more current available for a longer period of time. 6 volt batteries have heavier plates, thus allowing for more capacity as well as longer battery life.
Now you have to take into consideration -- 1) SPACE, 2 6volt batteries take twice the space. 2) WEIGHT, 2 6volt batteries will weigh at least twice as much.
Now if you have the space and the additional weight will not be a problem then go with 2 6volt batteries.
Browzin is right as far as he goes, but there is much more to it than that. When you connect two batteries in series, as you do with two 6V batteries in a 12V system, you effectivly create one very large 12V battery. It does have much heavier plates than do 12V batteries which is easy to see since one of each will be very similar in size. Also, with batteries in series, each cell will see all of the current flow that goes into or out of any other cell. That does one good thing and one bad one for you. Since they are in series each cell will always be charged to it very maximum stroage capacity, with no effect from the other cells. But the negitive is that if one cell should fail open, none then work. Open cells are pretty unusual today, but can happen. If one cell should short (much more common) it won't matter how they are wired as the result will discharge all connected cells, no matter how they are connected.
There are those who will argue that two 12V batteries in parallel are better, and there are a few things that are true about that. If one battery should fail, with two 12V you would have the opition of disconnecting one battery and still operate, while with two 6V in series you do not. But, both batteries should always be replaced at the same time in either configuration so most people choose to go to the series 6V batteries for the much greater capacity.
The point that Browzin makes about size is also valid. The 6V batteries used in an RV are taller and slightly differently shaped than are a similar size of 12V battery and so if you have a confined battery box, you may find that the two 6V will not fit. I am a strong supporter of the 6V configuration, yet do not use it because my coach batteries are under the entry steps and there just is not enough highth to put a pair in!