If the batteries are in parallel, it doesn't matter. Note that the gentleman in the next post suggests that it does matter due to resistance between the batteries and under high current discharge conditions, it will create an imbalance. I suspect there would be a discharging imbalance no matter how good the connections are as no two batteries are going to behave identically. Assuming the two batteries in parallel are right next to each other and electrically bonded in parallel with large cabling or buss bars, I don't know if connecting positive to one battery and negative to the other battery would actually make a significant difference. In all fairness, I've never connected a load where positive was connected to one battery and negative to a different battery in parallel, but I don't think the additional resistance between the batteries would cause significant drama.
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