When batteries are hooked in series, you'll have a harder time keeping them balanced. Even due to manufacturing tolerances, if one battery has a slightly lower capacity than the other, then that battery will drain faster because it's having to source the same current as the "stronger" battery even though it's voltage may be lower. It's also be an exponential decay on the weaker battery. Torwards the end, it'll just turn into a parasitic load on the system when it gets really low. When they are hooked in parallel, they will keep themselves balanced naturally.
As for your deep cycle selection, why not go with a group 29 marine? If I recall, they are the same size and offer a higher capacity. But they also cost more. I guess it could be a future upgrade. You wouldn't have to re-do a mounting system because they are the same size...