Yes they do charge. Ive also seen quite a few guys at flamingo take their boat batteries out and charge it using jumper cables while leaving their truck running.
Marine Battery Maintenance Boatus Magazine
Do boat batteries charge while running. Changing the rectifier is a pretty easy thing to do yourself and the part is reasonably priced. Almost all outboards that have electric start and that were built in the last 20 years will have either an alternator or a stater that charges the battery when the engine is running. If they rigged up the power winch adapter plug and put their battery switch in all they could charge both their starting and trolling motor batteries without having to take the batteries out of the boat. No voltage drop so both batteries get the full charge. The battery youve selected powers all of your 12 volt dc systems engine ignition lights electronics stereo etc. Deep cycle batteries are more for things like trolling motors and pumps.
At what capacities and loads they charge the batteries is another thing. Whenever the outboard engine is running the combiner will share the charging output with the trolling battery. You can use it in or out of the boat which makes them dual purpose they are a bit more expensive than portable styles but they are permanently installed in the boat adding convenience. Pretty much all outboards that have an electric start will re charge the battery as it runs. On board marine battery chargers allow you to charge the boat battery while out on the water. If the boat is running and the battery is not charging then the alternator rectifier might be faulty and needs to be changed.
In the bow i have a 27 series deep cycle that runs the trolling motor. No connection between the two batteries right now. Once you shut the engine down the same battery will be providing power. Using a portable marine battery charger requires more effort. When the engine is off the trolling battery is separated from the starting battery and will not accidentally discharge it. The motor is usually ran from a cranking battery.
Theres a battery in the back that i use for starting running lights depth finder etc. I have a 16 foot lund with a 60 hp merc. The alternator in the outboard does a fine job of keeping that battery topped off. Your system works something like this. If your battery is not charging then there could be a few different reasons why. The alternator will charge your battery back through the switch so the battery youre using underway will be constantly recharged while the engine is running.
Completely automatic no switches to worry about.