Have you upgraded the wiring IE done the MAD mod and bypassed the ammeter? If they are both "one wire" they you should have no regulator wires?? to deal with
I don't understand what you are saying, you say "both are one wire hook up" but you are talking about a regulator.
If the old one IS external regulator, you basically just "safe" those wires off. do whatever you want cut them, tape them, etc.
Do NOT put a one wire, and especially a "big amp" alternator on "stock" wiring harnesses.