H'm. This is important so lets look at the stock wiring for minute.
The car has two power sources, alternator and battery. The factory wired them together at the main splice. The main splice is where all of the other circuits are tied in except the starter motor. Whether the alternator is providing power or the battery is providing power, power goes to the main splice and then wherever needed.
So if the alternator output is cut and taped, and the battery feed/charge connects to the alternator, this is what I'm picturing.