It depends on your configuration. If you have two part cooling fans, both can be connected in parallel to the fan controller pin. If it's for the fan on the hot end, connect it directly to a 12V psu, it should always be running.
The part fan cools the filament as it just goes out of the nozzle.
So the fused filament stays in place. It's mostly usefull for overhangs, bridges, and small areas, like sharp ends (pyramid top alike).
