You have to configure a spare port. You can use the Fast Idle port (say you have an IAC stepper motor instead or a PWM solenoid) for something other than fast idle . Or think, but not familiar with, the version 3 has some extra spare outputs. Here's the link to configuring them, I haven't completely read and understood it yet though.
It works really well. On my setup, the fans come on at about 92 degrees celcius. I also set up the fans to only come on if the engine was above (I think) 500rpm. This ensures the fans aren't running when you are cranking. I used a spare port - the warmup LED in my case.
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