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Its always in your best interest to operate with all your batteries in series. The general rules, from what I heard are something like this. If you have a 100Ah battery, don't pull more than 80A (not sure if its 80% or lower) from it to maintain good battery life. If you have 12 of these 100Ah batteries, you can run 144V or 72V or 36V or whatever parallel setup you want. However, you'll want to limit current draw to a max of 960 amps (80% of 1200). 960A at 144V is a heck of a lot more power than 960A at 36V, and you don't sacrifice capacity or anything else to get more power. However, your components are just a lot more expensive.
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