Im relatively new here, and recently purchased a cig 20 project boat. Boat runs great but the alternator is not charging the batteries. I notice this first when the trs wont go in or out of gear (low voltage), then eventually it will just shut down. I have had the alternator checked and it checks out fine. The batteries are new, and everything appears to be hooked up properly. Does anyone have any ideas on what to check next?

Check the fuse at the starter

with the boat not running, check the voltage at the alternator's main post. it should show you battery voltage, if not. check the wire back to the starter, it should be a orange wire about 8ga. with the engine running it should show 13.5 to 14.0 at the post on the alternator.