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The current is always divided amongst how many batteries you have. If you have two batteries and are using 100A, you are pulling 50A from each battery. It doesn't matter if they are in series or parallel. You have two batteries that are splitting the amperage draw. In the series setup you will be getting twice the power and half the battery life. In the parallel setup you will get half the power, but twice the battery life.
Resistance is something to think about, but I think its fairly small when you figure in the bigger picture.
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