Use your OEM wire diagram. Hook the single wire from the alt to the same location as the 'bat' wire from the old regulator.
You will need to add an 8ne10306 or similar dropping resistor, after the OEM ballast resistor in order to use the oem 6v square coil.
If the alt tested good.. but you get dead batteries.. either the charge wire ain't hooke dup.. or you aren't running it up to a high enough rpm to get it to self excite.
That's why i like the 3 wire alternators.. they excite at a nice low rpm.. like 400 or so..