It is intended that you use the Phateks PWM Hub as the connection point for ALL your case ventilation fans. The Hub requires connection to ONE mobo fan port, and all other SYS_FAN ports of a mobo are not used.
The instructions point out that the Hub MUST have a valid PWM signal. This is what its cable that ends in a female 4-pin fan connector is for. Phanteks points out that some mobo makers have provided as their SYS_FAN ports what amount to "fake" 4-pin ports. They have 4 pins, but they actually operate exactly as a 3-pin ports would in Voltage Control Mode and the fourth pin has NO PWM signal - it is useless. Thus as a precaution, Phateks advises that you plug this cable into the CPU_FAN port instead because almost all modern mobos use real 4-pin ports for this function, with a valid PWM signal on pin #4.
I disagree with Phanteks because ideally the case ventilation fans should be controlled by a SYS_FAN port which is guided by a temperature sensor on the mobo. (The CPU_FAN port is guided by a temperature sensor inside the CPU chip itself, and is not really ideal for governing case ventilation.) However, I agree with them that this opens up the possibility that the Hub might not operate correctly with some mobos. So I have a different suggestion, although a bit more complicated.
1. Plug your CPU cooling system into the CPU_FAN mobo port and let it control that cooler.
2. Plug the PWM Hub into one of the mobo's SYS_FAN 4-pin ports. Plug the other cable from the Hub into a SATA power output connector from the PSU to get power for all the Hub's fans. Plug all your case ventilation fans into ports on the Hub, but make SURE to connect one fan to the white Port #1.
3. Boot into BIOS Setup and go to where you configure SYS_FAN ports, particularly the one you are plugged into. Check what Mode the port is using. Sometimes you will have no choice, or it may talk only about something like a slope of PWM per degree. BUT if it gives you a choice of using PWM Mode or Voltage Control Mode, make sure you set to to PWM Mode. Save and Exit.
Now observe your case fans' actions carefully. What should happen normally is:
(a) at start up all fans should start at full speed for a few seconds, then all slow down.
(b) If you have the computer do a lot of work, you should hear the fans speed up at heavier loads and slow down when idling.
If that is what happens, everything is OK.
BUT if all your case fans only keep running at full speed all the time, then the Hub is not getting a PWM signal to use. This will force you to shut down and go back to Phateks' way: move the Hub's 4-pin fan connector to the mobo CPU_FAN port. Move the case fan on the white Port #1 of the Hub to another port. Then plug your CPU cooling system into that Port #1 of the Hub. This will put all fans - CPU and case vent - under control of the CPU cooling system, but it will at least be automatically adjusted according to computer workload.
Now, about the last note on manual page 31. This all has to do with fan speed readouts. Interestingly, cooling and speed control functions do NOT need this speed signal - it is only for information and for failure monitoring. All fans generate a speed pulse signal (2 pulses per revolution) and send it back to the mobo on Pin #3 of the fan port. The mobo counts those pulses so you can see its speed, and it also uses that signal to warn of fan failure if NO pulses are being fed back. Now, most mobo fan ports can provide enough power for 2 fans, but not more, so people use Y-splitters to connect 2 fans to one port. BUT if the splitter merely connects all three fan wires from each fan to the port, the the mobo counting circuit gets TWO slightly different pulse strings overlapping and gets VERY confused with bad readings. So, any decent Y-splitter only connects to the mobo ONE of its fan's speed signals, and the other fan's speed simply is never measured. Extend this to the case of the PWM Hub which can have up to six fans on its ports. The Hub is wired so that ONLY the speed signal of the fan plugged into its white Port #1 is sent to the mobo - all others are ignored.
Further of this two-on-one concept, the HUB's ports also can be used with Y-splitters to connect two fans to EACH of its ports. It comes with a couple of these (in case you have more than 6 fans), and you can buy more. However, Phanteks advises that you should NOT use a Y-splitter and connect two fans to that one special white Port#1.