Ahh, I see looking at your pic again that this is an Explorer alternator. Correct?
If so this is actually a 4G just so you know. So yours will be just like the one in my picture.
In this case your wires are oriented like this:
1. The upper wire (the "black" one
%) ) is the Yellow w/white wire that is your battery sensing wire. It can be attached to your alternator's output post with the heavy gauge cable, or tied into the Painless wire of the same color (or just yellow maybe?) from the original voltage regulator harness next to your Green w/red wire.
2. The center wire is not used.
3. Bottom wire in your pic (the "black" one
) is the Green w/red wire that gets power only when the key is ON. This would be the same Green w/red wire in your Painless harness.
The center wire would have been the White w/black stator wire. This is unused in your case so can be capped off safely (shrink tubing is good) so it won't cause any trouble later.
Hope that helps.
Paul