Alternator control

Hey good day I have a quick question, do the Haltech elite controls the alternator or the charging system and if so how do you wire that to 2jzgte or a 90 supra with a 2jzgte in it. I have the 2500 elite. The problem I’m having is I’m running to cooling fans and whenever the fans come on the voltage goes out to 15 V and I know that is not safe at all

Does the alternator use a reference voltage, and where are you measuring the voltage(s)?