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Trojan 6v batteries are highly thought of but expensive. Most people go for a quality 12v which if cared for will last quite a while without the complications of wiring two 6v. You need to decide how much storage you need which depends on your usage pattern. ie weekend use/long passages/live aboard/fridge use/ night passages etc. Then look at price per capacity. I chose 75ahr because I have a small boat with few electrical gadgets. As you have previously had a single battery, I would think that you're a low user and could probably make do with a single 100ahr.
Dont know too much about fast charging so I'll leave that to the experts.
So what is complicated about linking 2 6volt batteries with a single cable to achieve 12 volts?