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Ok, so it just occurred to me, shall I use the starter battery just for the starter motor and the second battery for everything else including starter solenoid activation via the ignition circuit? What is the norm please?
I'd suggest (from experience and assuming that both batteries are identical) that you use one battery at a time for all power. At intervals of your choosing (say, every other excursion), swap from one to the other.
This routine will "exercise" and charge each battery in turn, hopefully giving you a recently used and charged backup battery for emergencies/failures.
I do not understand boats. We live in a very dry place where water is too precious to even drink.
I have a truck. The engine battery is just to start the motor. The accessory battery is a "boat battery" or deep discharge battery.
When the engine is off and the battery voltage is below 12.5V then a relay opens up and separates the two batteries. Now I can use battery 2 power while battery 1 remains hot to start the engine. After I start up the voltage will be above 13V and the relay closes to charge both batteries.
"Battery Isolator" I have heard complaints about battery isolators. They are in trucks, RVs, and in any auto parts store.
Will you be in fresh or seawater? Reason I ask is that both promote corrosion (since fresh is never truly ion free), just at differing degrees and speed.
That said, when on the water (of whatever flavor), I'm a big fan of prevention and simplicity. I suspect you've reached a point where it might be best to now make sure all your various connections are tightly secured and waterproofed. Even if in a watertight compartment, follow up by covering the battery terminals with this, or its equivalent. For the rest of the connections, cover them with "Liquid Insulation" or the like.
With any 12VDC system, even the slightest corrosion will present itself as significant resistance and degrade end user and charger voltage levels.
Thanks Guys, waterproofing and sealing is a great idea, and it's saltwater by the way, but when it comes to connecting the ignition circuit and starter solenoid would you do this on the start battery or house battery circuit?. Just leaving the 35mm cable only maybe from start battery to starter motor? Here are some pics of the boat (6m wooden) and engine (Yanmar 3JH25A). Just for interest I'll post some pics when she is finished