The black wire should be the wire that runs from the horn button in steering wheel. It attaches to one of the two prongs at the bottom of the horn relay. The green wire, I believe, runs out to your horns. There should also be a red wire, which comes from the battery and gives the relay power. Mine also has a black wire that runs from the relay to a connector on my firewall. That supplies power to my Rally Sport lights, so if you don't have an RS you won't have that wire.
The red wire that attached to your original alternator is connected to the red wire that attaches to your horn relay. So basically, this red wire runs from your alternator to your battery, with a junction at the horn relay.
I have a one-wire alternator, and just used that red wire. The other wires that went to your alternator were from you external regulator, and don't need to be used anymore.
Hope this made some sense..