If you are using the standard single phase alternator, the regulator/rectifier (Podtronics, Boyer, Tympanium, etc.) will have four wires. A red, a black, and usually two yellow. The red goes to a good ground, the black to the (-) battery, and the yellows to the green/white and green/yellow leads of the alternator stator. If the bike was converted to negative ground, then the black goes to ground and the red to the + side of the battery.
If the charging system has been upgraded to the three-phase system, you will have three yellow leads and three leads from the alternator.