I would personally let your motherboard take control of the fans. Why I personally recommend this is because your motherboard can detect all CPU, GPU and so on temperatures, then your motherboard would decide to tune up or tune down the fans. With the CPU it's just controlling how your CPU feels while you can have your fans spin for what your motherboard is detecting. Makes sense to me
By default the mobo controls them and allows you to manually set them to whatever you desire, i.e. if it seems to be running a bit hot, you can raise the fan levels through the BIOS or packaged software that comes with the mobo