The external regulator has three terminals: There is a ground, often the case itself, a "hot" wire that goes to the ignition (purple), and a field connection that goes to the alternator field input, usually a 1/4" push-on, or maybe a small stud. The actual alternator output, the large red or orange wire, does not go to the regulator (usually). It goes to the battery, perhaps thru a battery switch.
The new alternator has the regulator inside. The field connection is internal, and the regulator itself is probably powered from the alternator output, which is connected to a battery. There is likely another small terminal, that should be connected to the ignition (purple).
One caveat: If you use a diode-type battery splitter, then the alternator current flows through the diode to the batteries but current cannot come back the other way to power the regulator/field circuit. The alternator doesn't "turn on" since the regulator needs output to run and there is no output.
The solution here is to put a diode from the ignition to the alternator output. This supplies power to the regulator whenever the ignition is turned on. You can see how I did it on my website,
http://www.geocities.com...Wiring_32_Marinette.pdf
If you don't have diode-type isolators (they did not come from the factory) then just leave the alternator output alone, and hook up the ignition to the small terminal if needed.
I can perhaps be more specific if you can tell me the make and model of the alternator....
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida