If it's an internally regulated Delco alternator, one of the small wires is the field excitation and the other is the regulator sensing wire. I believe field excitation is the #1 wire. Typically this is connected through an idiot light to a 12v source that is hot when the ignition is on and disconnected when the iginition is off. The regulator sensing wire is connected somwhere in the system that it can measure the voltage and adjust for voltage drops to make sure the system is getting full power. Typically this is near the battery supply to the fuse box, although some just connect it to the alternator output. It is important that the excitation wire be disconnected when the ignition is off or the alternator will feed back through the idiot light and power whatever its connected to. That's why 3B suggested connecting it to the accessory position of the switch.

To learn a lot about this in a short time, I recommend the MAD Electrical Tech Section .

regards,
Leon