The Duet has three PWM controlled fan headers and two Always On fan headers.
A PWM (Pulse Width Modulation) fan connection is for fans you wish to control the speed of, for example a print cooling fan.
An always on fan is for something like an electronics fan - always on when the printer is on.
Some fans are more compatible with PWM control than others. If you have trouble varying the speed of a fan, check the documentation for changing PWM frequency.
The polarity of the fans is important - don't connect them backwards.
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