If you are using the option on one fan header to implement a custom "fan curve", that curve applies ONLY to that header and its fans. Then the question to consider is: WHAT is the fan cooling? IF it is the CPU chip cooler, then the CPU_FAN header VERY likely does NOT allow you any choice of which temperature sensor to use. IF this header and its fans cool the case, then the header always should use the motherboard general temperature sensor, and NOT the CPU internal sensor. SOME mobos have additional sensors on specific components as a choice, but those normally are to be used only for a header where you have aimed its fan to that particular mobo component.