Batteries: Two-6V In Series, or Two-12V In Parallel ???

2 12 volt batteries in parallel will pray from each other giving you a parasitic power loss proportional to the consumption. To be able to make it work efficiently you will need battery isolators.
2 6V don't have this problem. I did the same change twice, the 6V proved to last much longer because I did not have the isolators.
Good point on the high. 6V batteries are taller. All RV manufacturers keep that in consideration, but your battery tie-downs might not work any more.