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Re: Replacing 12 volt batteries with 6 volt
"I am replacing 3 batteries that are configured as 2 for the house bank and 1 for starting with 2, 6 volt Trojan batteries"
Your two new 6V batteries can be combines into one 12v battery, or battery bank, whichever term you prefer. That one new battery can be used to replace your previous house battery bank (of 2 twelve-volt batteries) and you can always leave one of the three old batteries as a dedicated starting battery, if any of them has any life left in it.
Or, you can simply use the two new batteries as your only "battery bank" and wire it up to position 1 or 2, leaving the other one unused, on your battery switch. If you're going to do that, I'd suggest replacing the switch with a simple "On/Off" type, which eliminates any possible confusion or damage from someone selecting the wrong position (i.e. "2" if there's nothing connected to it) on the existing battery switch.