Ok, after a little research I've figured out how the fan controller's cables are supposed to work, so my question now is:
Am I better off leaving the chassis fans plugged directly into the motherboard and let the system handle it, or should I plug them into the fan controller switch and control them manually?
Am I better off leaving the chassis fans plugged directly into the motherboard and let the system handle it, or should I plug them into the fan controller switch and control them manually?