I realized I have a spare port on my motherboard to control an extra pwm fan (in addition to my blower fan).
Given the option, would it be better to use it for my hotend fan or for my part cooling fans? I’m primarily looking to reduce noise while printing (I have a pin completely cutting power to the fans when the machine is idle).
The hotend fan should be running at full blast whenever your heater is on, mostly to keep the PID loop happy. If the fan is way overkill for your hotend you could use the PWM port to set it to run permanently at a lower speed, but otherwise there is no need to ever adjust it, and probably the better thing would be to buy a smaller more silent fan anyway.
Back when I was using a glass bed, I rigged an extra 120mm fan to blow on that after a print was complete to release faster. Now that I don’t, that pin controls my enclosure light brightness.