Any recommendations for an onboard charger and batteries would be much appreciated. From my understanding what the charger will do is take power from your outboard’s alternator and use it to maintain the battery life of your trolling motor battery?
Generally its not a great idea to use the same battery for your trolling motor and starting your outboard. Maybe you don’t have room for separate batteries, but if you do, I’d dedicate one as a cranking battery and use that for your outboard starter, electronics, pumps, lights, etc and then dedicate a deep cycle for your trolling motor. If you use the same battery, there is a risk of running the battery too low to restart the outboard.
As far as batteries, that’s a big can of worms to open up. There are three types: standard lead acid, AGM, and lithium. They range in price from 100 bucks all the way up to about 500 bucks.