You just brush the positive to positive of the ALT to the VR or something. You can use a very small gauge wire too, so there is not a bolt of current. It just needs to know what's up and what's down (i.e. + -).
This from a different how-to site:
After the installation of a battery, generator or voltage regulator follow these procedures. The terminals on the voltage regulator are labeled with letters and this is where you will do the polarizing procedure. Both of the components will have battery power so do not start the vehicle or turn on the ignition switch before polarizing them. You will need a small piece of wire fourteen or sixteen gauge with alligator clips on the ends. Find the "B" terminal on the regulator and attach one of the alligator clips, find the "D" terminal and touch the terminal with the other alligator clip. You can touch the terminals a few times and it will produce a soft light spark. Under no circumstances touch the "F" terminal or any other part of the regulator or you could damage the regulator.