In an early dual fan setup, the ECM turns the first fan on and off, but AC and high temperature are also "monitored" by sensors, which govern both the second fan, and the first fan in the case of an AC "override". The ECM doesn't have anything to do with the AC and high temperature switching, those are just temperature and I think head pressure switches.
Later stuff also has a high speed function built into the ECM's that shuts the fans off regardless over a certain MPH.
Great thing about these setups, is that you can eliminate the head pressure switch (if not running AC like me), there are a multitude of different temp rated switch temperatures you can get, and the ECM can be re-programmed with the on/off temperatures of the first fan.