Just to make sure we're on the same page, I'll assume you mean one of these:
If so, let's go to this pic:
(click pic to enlarge a little)
IF you have the terminal marked #1 (not all do), this is an additional ground, to supplement the ground from the mounting bolt (#5).
Numbers 2 & 4 are where the alternator leads plug in. Doesn't matter which, as the voltage from the alternator to the rectifier is AC current.
Number 3 (center terminal) is the "hot" lead (converted to DC voltage), and splits off in two leads, one going to the system, the other going to the Zener Diode, which acts as the voltage regulator.
Now, a few things to be aware of:
When removing or installing the rectifier, ALWAYS use a wrench to hold the "bolt head" (under terminal #1 in the illustration) to keep it from turning while you loosen/tighten the nut.
If you don't do this the "plates" will turn, breaking their internal connection(s).
In that case, you might as well take it off and throw it in the trash, and go buy another one!
Make sure the mounting is contacting clean, bare metal (no paint, rust, etc).
I usually use a piece of Scotch Brite and shine up the mounting area, put a dab of dielectric grease (available at auto parts store) and slip an external tooth lock washer over the bolt threads before inserting it into the hole and tightening with the nut:
The teeth of the lockwasher dig into the mounting surfaces, giving a better electrical connection.