This isn't rocket science people.
The alternator output probably connects to the starter lug or maybe the battery switch. The alternator sounds like it has an extra ground wire attached. Years ago I added an extra ground wire on a car to reduce the voltage drop, easy, cheap and it worked. I'm thinking about doing the same on my boat but I want to measure the voltage drop first.
The charger needs replaced, easy.
Post some more photos and I'm sure this can all be cleared up.
The alternator output probably connects to the starter lug or maybe the battery switch. The alternator sounds like it has an extra ground wire attached. Years ago I added an extra ground wire on a car to reduce the voltage drop, easy, cheap and it worked. I'm thinking about doing the same on my boat but I want to measure the voltage drop first.
The charger needs replaced, easy.
Post some more photos and I'm sure this can all be cleared up.