You REALLY should connect the rad fans of the H100i system to the fan connectors coming out of the pump unit. The iCue software controls those fans through those connectors, based on the cooling needs of the CPU chip, as sensed by a temperature sensor inside the CPU. There also is the matter of a secondary function for CPU fan control. Their speed signals are monitored for a NO signal situation, which is interpreted to be fan FAILURE and normally triggers rapid warning messages and perhaps quick actions to limit or shut down your system before the CPU can overheat. For that purpose, the correct fans (on the rad) need to be plugged into the wires designed for that - that is, the ones from the pump unit.
NOT all fans are the same. Control of the speed of case cooling fans is based on a DIFFERENT temperature sensor built into the mobo, and the iCue software reads that sensor and uses it to control all the fans connected to the Commander Pro. Thus the CASE fans need to be plugged in there, abut NOT the CPU cooler fans (the ones on the rad).