dhale :
csf60,
So it seems then that - I can run the H100i with 2 pin wires connected to the 4 pin CPU header if I open Corsair link as that will give me fan control for slow-medium-fast correct? What if I don't use the corsair fans and use the Noctua AF-A14PWM fans instead?
We're mixing things a bit, let's see. The 2 fans (SP120) that come with the H100i have 4pin connectors (I made a mistake before saying they were 3pin, but I took a look inside my computer and they are in fact 4pin). These can be connected to the motherboard 4pin fan headers and you can control them by any software you want within windows. However, they come with a special adapter to connect them to the pump, which then by usb connects to the motherboard. This allows you to use Corsair link to manage the fan profiles. Yes, Corsair link gives you fan control for slow-medium-fast and every custom profile you would like to make. It has more options too such as configuring the color of the pump LED.
The 2pin connector i talked about is meant to be plugged into the motherboard CPU fan header but it serves no purpose other than telling your motherboard: "hey, I have a cooling solution up and running even if no fans are connected to you"