2000 Yamaha F100 Alternator Output

I'm working on rewiring my boat. Motor is a F100 main. The current setup didnt have a separate wire running to the battery for the alternator output. This is my first outboard boat. Do they just backfeed the alternator amps down the main power wires, or should I have a different feed?

[boats.net]

It charges by way of main battery cables, there is no second lead.