I'm pretty sure that second wire is the ground/negative wire from the alternator (I don't have my wiring diagram handy). That would make it the return path for all the current in the bike's electrical system (a circuit must go in a circle).
I'll double-check my wiring diagram tonight, but the easiest way to check would be to put a voltmeter on the red wire and the orange. If it reads anything but 0 (probably 12 V with the bike off, 14.5 with it on), then the orange wire is ground. If it's another positive supply, then it'll have the same voltage as the red wire, and the voltmeter will read 0. Or you could test the orange against ground, which would be 0 if it's ground, or 12/14.5 if it's a supply.
I don't think anything but the starter motor actually uses the frame for both ground and negative (all components are grounded to the frame, but have separate negative wires). That means there needs to be at least two wires from the alternator.
Dave