I disagree.
There really in only ONE reason that the Hub has one of its ports (the orange one) designated for the CPU cooler. On some earlier mobos ONLY the CPU_FAN header could supply the PWM signal on Pin #4, and that is REQUIRED for this Hub and its fans to work. So telling you to hook it up that way guaranteed it would do its job.
OP, your mobo CAN use the new PWM Mode (that is, it WILL put out the PWM signal etc.) on BOTH of its fan headers - you just have to be sure the headers are configured that way. So you can leave your CPU cooler connected to the CPU_FAN header, and then connect this Hub to your SYS_FAN1 header. But be SURE that all of the FANS you add are of the 4-pin (PWM) style, because only that fan type can be used with this Hub and a PWM signal from the mobo. Then, be sure also to have one of those case fans plugged into the orange Hub port #5. It is the only port on the Hub that will send back to the mobo SYSFAN1 header a fan speed signal. The speeds of all the other fans on this Hub will be ignored because the mobo header can only accept ONE fan's signal. This has NO impact on ability to control fan speeds.
Once you connect the HUb and all those case fans this way, go into BIOS Setup and see the manual p. 24. Note that you must choose first which of the two mobo fan headers you are configuring. Choose the SYSFAN1 header. Set its Speed Control to Normal, Use Temperature Input to the motherboard sensor, NOT the one inside the CPU chip, Control Mode to PWM. Remember to SAVE and EXIT to save your new settings and reboot.