There's a larger wire on the altenator's post (red), the smaller ed wire goes to the larger red wire. Those two wires I just wrote about are the furthest apart. The white wire (in between the two red wires) goes through a idiot light and then to the ignition. Does your system have an idiot light? If not, I don't know how else it could work. The light has to be good in order for it to charge.
I have also seen it where a person hooked up the + coil wire to the smaller red wire on the altenator which went to the igniton, his engine wouldn't shut off.