I assume you're talking about converting to an alternator using an internal voltage regulator. You still need the heavy red wire with the ring terminal that connects the post on the back of the alternator to the battery, but you can unplug the three-prong connector. If you want your alternator warning light to work, though, you need to connect a wire from the D+ push-on terminal on the back of the new alternator to the D+ terminal on the three-prong connector (or, instead, run a new wire directly to the light in the instrument cluster).
I'm doing this from memory so if I'm wrong, someone please bitch-slap me.