Corsair suggests that you connect the two fans to the control module via y-connecter. However, doing so under linux makes it impossible to control the fans and they will always run at 100% RPM.
If you connect the 2 fans to the motherboard (as chassis fans) you can control the fan speed as you normally would via
fancontrol (see: How to control fan speed?) , significantly reducing the sound level.
Connections would be as follows:
Fans x 2 -> Chassis Fan(s) on MOBO
Corsair Pump control -> CPU Fan on MOBO
USB > USB Header on MOBO
If you're not overclocking, the cooler unit is very unlikely to require management at all. For example, I have an i7-3930k running at stock frequency and the temps are staying between 32-40 at all times. Case is practically silent.