Right, one short piece just connects one prong right to the "batt" stud, and the other goes to a different destination.
I know which wires I need to connect to those prongs, I just don't know which to use.
The one labeled "R" is on the left when looking at the back of the alternator. The one labeled "F" is on the right.
According to the schematic you posted I should connect the one labeled "F" to the "batt" stud.