If I just want to run my fans at a certain PWM duty cycle,

If I just want to run my fans at a certain PWM duty cycle, or allow them to be controlled by the cooling function in Cura, how should they be configured? Any hints or a link to where it’s documented much appreciated!

Here’s the section you want in your local.cfg with examples. In this case fan-1 is controlled by Cura with M106, and fan-3 is started by the temperature rising on the extruder e reaching the threshold temp (default is 60 degrees):

[Cold-ends]
connect-therm-e-fan-1 = False
connect-therm-e-fan-3 = True
add-fan-1-to-m106 = True
add-fan-3-to-m106 = False