OK, so looking at the manual for your motherboard, the Water Pump Fan Connector is where you plug your H100i into (aka CPU_OPT header). And if you don't want the H100i to control the fans on it, then you can connect the fans to the CPU Fan Connector instead of into the H100i AIO.
But most people I gather just plug the fans into the AIO, then the AIO into the Water Pump Fan Connector and then use the iCue software to control what's needed.
:: edit ::
Reading further into the manual, you are correct in bringing up the Chassis Fan connector, as it looks like that can be used for the AIO as well. But typically most use the CPU_OPT header since it's easier to tell if it's the CPU one you are reading temps etc off of.
I imagine the Chassis one is a second one that is used by those having a second AIO for GPU or something.