Whichever is connected to the pump should maintain a speed >2000 rpm. The PWM fan (4 pin) should be able to be controlled via AI suite or in bios. You do not change the q-fan control unless you have a 3 pin fan you want to control. If your Fan xpert cannot control your fan make sure it is plugged in correctly and make sure your fan xpert is working properly IE does it control your case fans or are those static as well?
Also the speed of the fans is dependent on your temperature curve you set. If the temps are low enough the fans wont spin. Put your setting to full speed and see if your fans run.
i7-4770k @4.2 | EVGA 780ti | Maximus VI Hero | Seasonic 1000W Platinum | Seidon 120v AIO
Trident X 16GB 2400 | Samsung EVO 500GB | Seagate Barracuda 2TB | CM 690 III
Logitech G400 Mouse | G710 Keyboard | Razor gaming headset
ROG Swift pg278q G-Sync Monitor