With generator it can be set up either positive or negative ground. Most generators were positive ground from the factory but will work either way if properly connected.
You say 2 wires to the coil. Does this have a ballast resistor between switch and coil? If so, the oher wire could come from start solenoid and is designed to bypass the resistor when starter is engeged, thus increasing voltage to the coil to give hotter spark for starting.
We have a 302 wired this way.