Using two 6V to replace your house battery, and still keeping your starter battery will require three spaces and additional wiring and connectors, doable, but it's not convenient to install, or maintain. Not to mention quite unnecessary for your stated needs. And not a great advantage (but there are some) over simply installing two equivalent 12V house batteries plus your starter battery.
If you are considering replacing both of your 12V batteries with just two 6V batteries, don't do that either- you will then be giving up a 12V backup in case of failure of one of them, and depending on your charger setup, it will be more complicated to deal with as well.
Does your charging system charge each battery individually (two leads from charger to each battery, a total of 4 charging output leads?) or are they charged together as one?
If they are charged together as one, then replacing both batteries with two matching deep cycle batteries is another option to consider as well. You could wait until the starter battery fails (partly depends its condition and on how old it is) and replace it with a deep cycle (same brand and size as the other one) at that time; although that does carry with it the risk of placing the longevity of your new deep cycle in jeopardy due to charge mismatch. A deep cycle battery in the size we are discussing will have ample capacity to start a modern outboard the size of ours, and will suffer no harm doing it.
And if you are considering going to just one 12V deep cycle battery consider this... Even if you do not utilize them fully with power-drawing accessories, having two batteries does not double your cost over time of having just one, because, if managed properly, you will be discharging them each less than you would a single battery, which extends their life, meaning they will need to be replaced less frequently.
-Brian.
