I have 2 large fans in my case it's mATX case the key components are:
Asus H97M-E Motherboard &
Hydro Series™ H55 Quiet CPU Cooler
Now the motherboard has 3 (4 pin) connectors for CPU Fans and 2 extra fans. 2 pins are taken by the water cooling system and one pin is taken by the default fan that came with the case.
Everything works fine however the BIOS is showing fans spinning at 1500-1600 RPM pretty much at maximum and the CPU is not even being overloaded it's at cool 23*C which is pretty low for new gen top level i7.
In BIOS I set all my fan control settings to Silent but these fans are going all wild no effect only thing is if I moved the fan settings from DC to PWM they go crazy they speed up even more and get even louder. I mean the PC case is now so freaking cold to the touch.
1 More thing the motherboard did come with a controller/device that allows you to throttle the fans at the back of the pc it has 4 cables two go to power unit the and two are male connectors where fans connect but they are (2pin) where as fan connector are female (3pin) but this can't be the way to control fans can it ?
I had wrongly connected the cables. Basically with water cooling system you get two cables one from the head that goes on top of CPU (pump) and one that is for the cooling system fan. On my motherboard I have 3 FAN Connectors however 1 is named CPU_FAN previously I had the pump connected to the CPU_FAN and the cooling system fan connected to FAN1 connector.
You have to connect the cooling system FAN to CPU_FAN and you connect pump to any other connector for me it was the 4 pin FAN1 connector. After that PC only get's a bit loud for few seconds after boot or very heavy loads.