Check and clean as needed all of your grounds, the battery is a chemical based storage devise that makes the voltage that the vechicle runs on. The current flow from all batteries flows out the negative terminals into the system and returns through the positive side of the battery If the grounds are not good it may lead to overcharging
The direction of current flow is nice to know on a theoretical basis. In real life it matters not. You need clean, solid connections on both the positive and negative sides, regardless.
