Let's review connections, plus possible adjustments NOT mentioned in your manual.
That Kraken X53 PUMP unit has a multi-headed cable from the pump, plus a socket on the side. From the multi-headed cable you must connect a wide connector to a SATA power output from the PSU. It comes with a SPLITTTER for connecting the rad fans to the mobo 4-pin CPU_FAN header. Ensure that one of those fans is plugged into the FIRST output of the Splitter that has all 4 pins . There is a 3-hole fan female connector to plug into the mobo AIO_PUMP header, and this merely sends the PUMP speed signal to that header. You use a separate cable supplied to connect from the socket on the side of the pump to a mobo USB2 header. This cable is how the CAM software utility communicates with the entire AIO system. You must download and install that software so it runs all the time.
If you use BIOS Setup to check the operations, the AIO_PUMP header may report to you the "fan" speed of your cooler system, but this really will be the PUMP speed, and it should always be the same - around 2800 RPM. IF there is a choice on this item for that header, set it to behave as a PUMP header and NOT as a fan header. Then check the CPU_FAN header and set that to use the "Normal" or "Standard" fan profile. This uses a default "fan curve" of speed versus measured internal CPU chip temperature to control the rad fan speeds according to workload. It will show you the speed of only ONE fan - the one connected to the only Splitter output with all 4 pins. This header should be set to use PWM Mode, not Voltage or DC or "Auto". If you have to make any adjustments here, remember to use Esc back to the Main Menu, then F10 to get to the Exit Menu and choose Save Changes and Exit.
With CAM working you should use that to see the pump speed and rad fan speeds, and make any further adjustments you think necessary.