You have misunderstood the plan for cooling components in this case.
There are TWO separate cooling systems. ONE is the CPU cooling system, and it cools ONLY the CPU. The OTHER is the case ventilation system, and only this system uses the PWM Hub included with the case. The CPU cooler does NOT connect to the Hub!
First, CPU cooling. You have the H1000i GTX system. It consists of a liquid cooler block mounted on the CPU, a radiator to mount in the case top, two fans for the rad, a couple of cables, and some software. Four cables need connecting in this system, and ALL of them go to the cooler block mounted on the CPU. Both of the radiator fans (which are supposed to be PWM type) connect to cables coming out of the cooler block. One wire from that cooler block plugs into the main 4-pin CPU_FAN port of your mobo. A separate cable connects from a socket in the cooler block to one USB port of your mobo.
The cooling system draws power from the CPU fan port, and also returns to that port some info about its fan speed. However, it does NOT use the mobo's automatic control system to regulate its fans. You MUST install the software that comes with the H100i GTX system. It takes info from the mobo on the actual measured temperature inside the CPU chip and exercises its own control of radiator fan speeds and pump speed, using the USB connection to communicate with the cooling system pump block. So this system uses its own techniques and equipment to manage the CPU temperature, and does NOT do anything for case ventilation. I suspect that the software supplied also includes a small app for the user to monitor and control the CPU cooling functions only.
Case ventilation is done by all your other fans and THIS is where the PWM Hub is used. That hub has one wire that plugs into a mobo 4-pin CHA_FAN port. Using that port's PWM signal it controls all the fans attached to the hub. It also returns to the port the speed of ONLY the one fan plugged into its Hub Port #1, the one that is white. It draws power for all its fans from a SATA device power output connector from the PSU so it does not overload the mobo CHA_FAN port. Among the various 4-pin fan hubs on the market, this one is different. It appears to use the PWM signal it gets to create its own group of 3-pin output ports operating in Voltage Control Mode. Obviously this means that you can use 3-pin fans with it. But it replies, too, on the backwards compatibility design feature that a 4-pin fan connected to a 3-pin (Voltage Control Mode) port WILL work under proper control. So both 3- and 4-pin fans can be plugged into any of the hub's 3-pin ports. ALL the fans plugged into this port will be under the SAME control - that is, the one PWM fan speed control signal it picks up from its mobo "host" port. This system is designed to control many (usually all) of your case ventilation fans from a mobo CHA_FAN port signal that is tied to a temperature sensor in the MOTHERBOARD, and NOT from the temperature of the CPU internals. So ONLY case ventilation fans should be connected to it.
Set up this way as designed, you will find that the MSI Command Center gives you control of the case fans connected to the hub. But control of the CPU fans is done through the software supplied with the H100i GTX system.