Re: Onboard Battery Charger Understanding
If your boat has an onboard battery charger, then there must be a 110v (standard household) plug somewhere also. The idea is that you can plug it in with an extension cord or a shore power stand and the batteries will maintain a full charge whenever the boat isn't being used. It is (more or less) a trickle charger for all 3 batteries when the boat is unattended.
When you're actually using the boat, placing the switch in the 'all' position gets power from all batteries. I would venture a guess that your engine isn't putting out enough power to adequately charge them all if they were low. Generally, people use a switch that is labeled 1, 2, ALL. You can set one of the batteries as a cranking battery (let's use #1). Start the engine with the selector switch on 1 or ALL. With newer model switches, you can start on 1 and then switch it to ALL and while driving, and the engine charges both batteries.
When you've anchored the boat and shut the engine off, switch to 2 (if that's your "house" or deep cycle battery) and run the radio, fish finder, GPS, whatever for the time you're there. If you wind up killing the 2 battery, you can switch back to 1 and you still have a hot starting battery to make sure you get home. Once started, switch to ALL and charge the low battery on the way home. This works even better if you have an automatic charging relay installed. That will tell the supplied power which battery is lowest and needs more charge, but it's not mandatory. If you kill the batteries on the ALL setting, you're dead in the water.
Once back at the dock, plug in the charger and it will top off the batteries prior to the next use. The third battery you have may just be an emergency back up of some sort. We would need to see if it were wired in with the others.
One thing to keep in mind. If you use the on board charger a lot, keep an eye on the fluid level in the batteries.