Yes you can hook 2, 6V batteries together in series and the second together also in series and then the two sets of series in parallel so this way you get 12v and the higher amperage by doing it this way.
Series is + to - and -to + for each of the two sets of 6V batteries then to parallel them you go + from one to + of the other bank and - of one to - of the other then to tie in to the system now go + from one bank and - from the other into the system. Taking the + from one bank (series) and negative from the other insures that all four charge equally.