OK, so we bought our new to us boat last year. This year I bought a new battery (batter #2 on the selector) (no surprise, surveyor said we would probably need a new battey this year). But, I was reading the manual and noticed that the #2 battery is meant to be the starter battery and the #1 battery is meant to be the house battery. We have the batteries different on our boat; #2 is the bigger (Group 27) dual purpose/deep cycle battery while #1 was labeled starter battery (Group 24) (when we bought her). The question is does it matter? When we leave her on Sunday we turn off #1 and leave #2 on. Should the batteries be swapped so #1 is the house batter and that's what we leave on using the selector switch? Not really sure why it matters and not sure why the manual says #1 is house and #2 is starter. Is there a unique connection between the battery labeled starter (#2) and the engine that I should be aware of?
It may not matter at all and then again it may matter depending upon how the system is wired.
For example if your alternator is wired direct to the house bank of the system or it is intended to "sense" the house bank you may have some charging issues to contend with. Also if you have an Echo Charger type device then it may be backwards.
Bilge pumps and other direct wired devices may be wired to the #1 position and be intended to run with a larger reserve bank if needed rather than a small starter battery. The start battery won't put up much of a fight against a needed bilge pump for very long.
If the system has the alt just feeding the common post of the battery switch, and you can choose which battery gets charged via the position the switch is in it will not matter much where you put the house battery.
We really can't be of much help without knowing more about how your system is wired and what you have for charge distribution etc..