97 Johnson 150

Does anyone know which wire provides the charging from the alternator to the battery while underway?
I moved my batteries to the port side and the only wire that was attached from the strand of wires in the wiring harness appers brown in color. Previous owner reported occasional battry discharge. Also What is the best way to wire the 2 so that they can operate in tadem at times and on their own at other times yet both receive a charge when engine is running
?
Capt Jerry