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After several hours of thorough research, I still haven't found a satisfying solution to my problem. My electrician bought a 90 amp alternator for my boat and I count on charging three batteries simultaneously and individually depending on the battery level of each. The most practical solution it seems, would be to connect the alternator directly to an ACR or a VSR to divide the amperage correctly and to avoid voltage drop by isolating the batteries and letting the current flow in one direction. What worries me though, is when the current is flowing to only one battery. Will the battery overcharge due to the too high amperage? Should I add a smart regulator to each battery or is the ACR system enough? Does the ACR system also make for a float charge? I hope that I wasn't too vague and I would be very happy with any advice on the matter.

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    i think that your title should say supplying 90A ..... motors draw current – jsotola Jul 7 '18 at 6:14
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You could do this, but you should leave one battery connected directly to the alternator so it functions correctly, then use a split-charge system for the other two batteries.

Companies who supply winches do split-charge systems and so do caravan builders.

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The risk of overcharging a weak 2V cell increases with age and total % of imbalanced ESR and Capacitance times current output. Therefore 50mV / 100A wire current sense using “Kelvin method” can be used to determine the imbalance charge.

If the batteries are connected prior to alternator for say 10 minutes then risk of imbalanced over charge is significantly reduced if batteries are OK. If a small lead acid “expired” battery is attached to an oversized Alternator , chances are that only 1 cell will outgas from excessive voltage (>2.5V) and it won’t accept a charge for long nor supply discharge very long. The ideal situation is that all cells are perfectly balanced much less than 1% difference in V and specific gravity. But once the weakest cell starts to differ, the aging from overvoltage accelerated faster. Thus it is best to have separate current limiters and cell balances to slow down the aging imbalance exponential effect but can be alternatively reduced currents as per above ( connect batteries until current sense drops then charge and monitor results)

Or get a smart ESR/Ah Battery charger that displays results with charger and load dump test.

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