You could have a room full of electrical engineers and ask that question and it may turn into a fist fight trying to settle it.
The John version goes like this.
Years ago it was better to have two 6 volt in series but today it is better to have two 12 volt in parallel. First it has to do with the quality of batteries and cables sold today. You can buy much bigger CCA 12 volt batteries today than you use to be able to. Also finding fresh 6 volt batteries that have not set on the shelf for a year can be a problem.
Second two 12 volt batteries may mask a problem and have you ruin both batteries where a problem with two 6 volt batteries will show itself and force you to fix the problem now.
In theory if both banks have the same CCA they will be the same. Remember you double the voltage on the 6 volt set and double the AH on the 12 volt set. So two 12 volt 200 AH batteries would be the same as two 6 volt 400 AH batteries if the cables are the right size.
You did not mention the AH or CCA of the batteries in question so we can only speculate.
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