Important question here. The installation manual for that system does not make clear WHERE you plug in the rad fans. I believe that the multi-headed cable that plugs into the main socket on the side of the PUMP unit includes one 4-pin male fan connector. I believe the kit also includes a fan motor SPLITTER so you can connect two or three rad fans to that single output from the pump. Is that correct?
You are NOT supposed to plug the rad fans into any mobo fan header, I believe. Control of cooling with this system is done by the maker's CAM software that you must download and run. That software pre-supposes certain connections. The speed of the PUMP will be reported at the CPU_FAN header, since that's where you are supposed to plug in the 4-hole connector from the pump. The speed of the RAD FANS is actually controlled by CAM through the PUMP unit, so that is where the fans need to be plugged in.
That leaves all your OTHER fans - the ones for case ventilation - to be plugged into the Hub you plan to use, and that Hub has a cable that plugs into your SYS_FAN1 header to get its PWM speed control signal. The RGB lighting cables from those fans go to the Hub's RGB ports. If your rad fans also have separate lighting cables, those, too, can go to the Hub's lighting ports.
With this arrangement you are not using the SYS_FAN2 header on the mobo. You say it does not work. IF you want to get it working, tell us what it does when you plug in one fan, and which type of fan? That is, 3-pin or 4-pin MOTOR connector.