Hottrucks, if I read your post correctly, it would seem that both batteries would be connected to the engine and electronics while underway. This means if the alternator dies underway, you will eventually end up with two dead batteries.
It is always best to start your engine with your cranking battery (1) and run it that way for a few minutes to recharge it, then isolate and switch to (2) to charge/use the rest of the day. That way, (1) stays full and isolated the whole trip for use as a backup.
When you kill (2) and can't start with it, switch to (1) and repeat above. If (1) is somehow too low to crank as well, then one can switch to BOTH to use boh batteries for cranking.
I would hate to have two dead batteries on the water...
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Sail fast, live slow!
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