I actually just went though this! I had my h80i connected wrong for over a year. Not corsair's fault, as I have a fairly advanced board (maximus viii hero) and their instructions are for less advanced setups.

First, ignore corsair instructions when using Asus fan control.

To begin, it Depends on your board. If your board has a waterpump header (such as the rog series), and the waterpump gets power from a 4 pin fan header, plug the pump into the waterpump header and set its control to disabled or full power. Then connect the fans to the CPU and CPU option headers, or CPU and another header if you only have one CPU header, (tucking the pumps fan power connectors safely out of the way), and run the qfan control setup.

If your board does NOT have a waterpump header, you have two options: plug the fans into the pump, the pump into the CPU fan header and turn OFF qfan for the CPU fan. Why? Otherwise the board cuts power to the pump and this is bad for it! However this will run the fans at full speed. The other option is to plug the pump into the CPU fan header and turn off qfan on that header and then connect the CPU fans to other headers and configure qfan for those headers.

If the pump gets its power from sata, then qfan doesn't matter.

Don't forget to connect the USB so you can use corsair link.

Once it's all connected, run the qfan thing in Windows and it'll detect and configure the fans and speeds for you (at least mine did with fan expert 3).

Hope that answers all questions and helps!!

PWM stands for "pulse width modulation", basically it means that the motherboard turns the power to the fan fully on and then fully off repeatedly, "pulsing" the power at a certain ratio of on vs. off in order to achieve a slower fan speed.

This method of slowing the fan is in contrast to the legacy DC setting, which simply sends a lower voltage to the fan.

The PWM setting is desirable because it gives the motherboard finer grained control over the fan speed. You can have a very high speed fan when it gets full power, and greatly reduce it's speed using pulses. The alternative of controlling a fan via reduced DC voltage is crude, the effect is non-linear, and you can't slow the fan down too much otherwise it just stops entirely.

But... to use PWM you need to have a fan that supports it and it must have a four pin connector. The fourth pin is the "pulse signal" which the fan uses to control it's speed. If your fan only has three pins, it doesn't support PWM, so it will ignores the pulse signal entirely and it just spin at full blast no matter what. Sure, that cools the system, but it also makes the motherboard's fan speed controllers totally useless.

Remember you want to move as little air through the system as you can get away with. Enough to cool it, but not so much that you turn the system into a glorified air filter.