1. You should have one large red (10 gauge or so) wire. This is the main power wire that goes directly to the battery. Make sure it is a heavy gauge since it has to carry the full output of the alternator (up to 100 amps).
2. The second wire, probably brown goes to a switched power source. This is the field wire that energizes the alternator. It must be switched, or else it will drain the battery overnight. Do not wire this into the coil power wire that you use to switch the engine on and off (a seemingly elegant solution), since once the engine is running the alternator will feed power back through this wire, which will then power the coil, and you won't be able to shut your car off.
3. The last wire is the lead for the sensing wire that goes to the idiot light in your instrument panel.