The Duet 2 Maestro has three controlled fan connectors FAN0, FAN1 and FAN2 plus one always-on fan connector. Make note of which fan is which from the Ender 3 board.
The fan voltage is jumper-selectable in 2 blocks. Ensure that the jumpers next to the fan connectors are set to the correct position. These jumpers select the voltage that will go to the fan pins. In our case, the Ender 3 uses 24v and the stock fans are also 24v, so we will leave the jumper bridging the VFAN pin with VIN.
In my case, the part cooling fan has the yellow (+) and blue (-) wires, and the hot end heatsink fan has unterminated bare red (+) and black (-) wires, and the case fan has a terminated red (+) and black (-) wires.
The part cooling fan will plug into Fan0, the hot end fan into Fan1, and the case fan into Fan2.
The always on fan connector can be used for another fan, or even LED lighting.
Further information on connecting fans can be found here on the wiki.
Connecting and configuring fans
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