Problem with case fans installation

You are on the right track, and the last two paragraphs for the docs you quoted above give you most of the info. To help understand and to get you set properly, read on.

The basic problem that the manual with the Phanteks PWM Hub worries about is that many mobos these days use 4-pin headers for their CHA_FAN headers, but actually use Voltage Control Mode to control any fans plugged in there. Meanwhile, the Phanteks Hub, like all 4-pin Hubs, MUST have an input from a true PWM Mode header, and cannot work with one of those Voltage Control Mode headers. To prevent your having trouble with this, the manual advises always using the CPU_FAN header because ALL current mobos can use PWM Mode on that header.

HOWEVER, the manual for your mobo says it does NOT use this type of odd 4-pin header. On p. 1-16 it shows that both of the CHA_FAN 4-pin headers have the PWM Signal on their Pin #4. So, you CAN use the Phanteks PWM Hub with this type of mobo fan header. Moreover, that is the right way to do this. You see, those CHA_FAN headers use the actual temperature measured by a sensor on the mobo to guide their control, and that is exactly what you need for case ventilation. (The control from the CPU_FAN header is based on a different sensor built into the CPU chip itself.)

The Phanterks PWM Hub is also exactly what you need for your purpose. All 4-pin Hubs avoid the limit on current consumption from a mobo CHA_FAN header. The Hub gets the power for all its fans directly from the PSU via a connection to a SATA power output from the PSU, and that can suuply MUCH more power than a mobo header can. The Hub then gets the PWM signal from the mobo CHA_FAN header you plug it into, and shares that out to all its fans, but this does not overload the header. Now, the Phanteks PWM Hub does something very different from most Hubs. Instead of merely sharing the PWM signal to its fans (and that would require that all the fans be able to use that signal, so they'd all have to be 4-pin design), it uses that PWM signal internally to create its own set of six 3-pin fan headers that operate in Voltage Control Mode. That is exactly what you must have to use 3-pin fans, which is what you have. Just an added note here - each port of the Hub can support more than one fan, and the Hub comes with two splitters to allow you to connect two fans each to a couple of its ports. So, out of the box, it can be used with 8 common fans, and you could even get a couple more splitters if you needed to.

The Hub makes use of a backwards compatibility feature of the new 4-pin fan design. A 4-pin fan connected to a 3-pin header operating in Voltage Control Mode (which is what this Hub does) will still be under control by the header, just as a 3-pin fan would. So the Phanteks PWM Hub can be used with any mix of 3-pin and 4-pin fans, and all of them will be controlled by the same PWM signal coming from the CHA_FAN header on the mobo that you plug the Hub into.

Bottom line. Get that Phanteks PWM Hub you planned on. Plug one lead cable into an appropriate SATA Power output connector from the PSU. Plug the fan header cable from the Hub into one of your mobo's CHA_FAN headers. Leave your CPU cooler connected to the CPU_FAN header. Plug all your case ventilation fans into ports of the Hub. Make sure one of those fans is on the white Port #1 of the Hub so that its speed will be sent back to the mobo header. (That is the only fan on the header whose speed will be reported to the mobo - you cannot "see" the speed of any of the other fans on the Hub.) Done this way, all your case fans will be controlled together by the CHA_FAN header of the mobo that you used, while the CPU cooler will be controlled separately by the CPU_FAN header.