Some folks like the concept of the A/B/Both/Off switch because if one or the other battery is having "Issues" isolation is fast and efficient.
Myself.. I'm not among them (I can isolate just fine with my wrench).
As for two 12's in parallel or 2 6s in series
The GC-2 6 volt Golf car battery is a true deep cycle (Can safely to to half full) 220 (giver or take a bit) amp hour set up... so you have 100-120 (Depending on the give or take) amp hours of usable power. Nice
Most 12 volt batteries (the GC-12 is an exception it's the same as above but less capacity) are MARINE/deep cycle. you can only use about 20-25 percent of the capacity safely
Group 24 75 AH
Groups 27 and 29 Just under/over 100
Group 31 130
Give or take a bit in each size depending on maker and model.
Source. Both US battery and Interstate battery
As for how to rig your rig... Up to you.
Some folks like that if one of the 12's in parallel fails. you still have the other one.. I have a mix of 6volt and 12 volt maintenance free. Eventually I'll move to more GC2 and less Group 29.