Water temperature is less spiky than the actual hardware temperature. Therefore it is better to use the water temp sensor for pump/fan control. The stock fan profile in the H100i is to aggressive for most, so it will cause annoying fan speed changes. Making a more boomerang shaped curve is usually a good thing. Then find a temperature above the normal spikes to set the steepest increase in fan speed.
If you want to keep your fans connected to the H100i you need to use the older Corsair software to set the fan curves. This profile is saved to the H100i directly, so there is no need to run the software constantly.
If you want to use the motherboard to control the fans, you have to unplug them from the H100i first, then connect them to the motherboard directly. Use CPU and CPU_OPT headers if you have both. Alternatively CPU header with a splitter. Then your fans will follow the fan curve set in the bios.
The pump rpm output from the H100i should be connected to the CPU header on the motherboard if you keep your fans connected to the H100i, so that the motherboard can warn you if the pump is not running. If you move the fans to the motherboard instead, you should move this back to the AIO pump header.