Battery Charging
DanThere really is no "way it should be."What you'll need to do is to trace the wiring to find out how YOUR particular boat was wired.Generally, folks do tend to have the alternator output go to the house bank, because the starting battery is almost always charged.Either through the use of the 1-2-Both switch or a battery combiner or an echo charger, the start battery would get some input if the alternator was wired to the house bank. Again, it depends on how your boat is wired. F'rinstance, if the output of the alternator goes directly to the start battery, you may not be able to use the 1-2-B switch to charge your house bank, or at least, you'd be running current an awfully long distance unneccessarily.It really is up to you, there are so many different ways to do it.Since you have a battery charger, which works from shorepower, that's a separate and different input to the batteries. The battery charger from shorepower has nothing to do with the output of your alternator. The shorepower chargers are generally wired directly to the battery banks.You may want to consider Nigel Calder's Boatowner's Manual, easily the best $50 investment you can make in your new boat, and one of the best in describing battery and charging systems. Of course, there' lots of that material on the web, but harder to read on your boat!

As a first step, I would recommend that you consider moving the output of the alternator from the start to the house bank, which always needs more input. Your start battery would be good for over 15 engine starts even without charging, since it only draws maybe 2 amp hours per start (high amperage, but for a very short time - like less than 30 seconds).Good luck,Stu