NEVER run batteries in parallel.
The problem is, if there is only a slight difference in voltage, one battery will discharge through another, which may cause overheating (due to large currents flowing between the two).
You simply run the whole thing one battery, and when it is empty, replace it with another one.
The similar goes for series connection, if batteries are not charged to exactly the same charge: when one battery is empty, there is a danger of reversing voltage polarity (because the other one will force current through empty one in opposite direction), this may destroy the battery pack.
However, this condition is easily detected (and avoided) because the overall voltage in this case drops below12 V
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