You need two things. The firmware has to have a pin definition for the extruder fan, and make sure it's not commented out. Then you turn it on in the slicer settings in the cooling section. This is generally a first layer setting and then a setting for the rest of the print. My guess is that one of the FET outputs Is already set as the extruder fan control, since that is a pretty standard output. So, most likely you just need to turn it on in the slicer.
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