Ok I got it. So for anyone that is i bit confused about the manual. Below the connections for the Corsair H110i GTX liquid cooler
SATA - Power supply
3pin Connector with 1 pin inside - CPU Fan Header
Two 4Pin Headers coming from the Corsair pump - connected to the two PWM fans
One of the 4 pin headers coming from the pump only has 3 pins inside because you only need the rpm reading from one of the fans.
They are both controlled by the same pwm signal.