Your two 6V BATTERY should be giving you 12VDC with around 200 + AHs...
I would rig a 4-way battery SWITCH (BLUE SEA SELLS THEM) which will let you select OFF-BANK1-BOTH BANKS-BANK2...
This will give you lots of AHs when you need it.
The mixing of batteries only come into play when you are charging them... With this switching arrangement you can switch in which bank you want to charge... This will also completely switch OUT both banks in the OFF position.
You converter/charge is probably a 45WATT model which is only good for two batteries anyway if you want the charge real fast using smart mode charging...
Roy Ken