You do not need to use the PUMP_FAN1 header. In fact, for use in general case ventilation, that would be the wrong place to connect those fans. That header and the CPU_FAN header use the temperature sensor inside the CPU chip to guide them. But the four SYS_FAN headers you have use a different temperature sensor on the motherboard to guide them, so that is what you should use.
The instructions for the Phanteks PWM Hub say to plug it into the CPU_FAN header. This is NOT necessary for your situation. That instruction is only to be SURE the Hub receives a PWM signal from its fan header, and some earlier mobos did not provide that signal on SYS_FAN headers. Your mobo CAN do this, but you need to make a small adjustment. All of the SYS_FAN headers are set by default to use the older DC Mode of control.
To start, see your manual p. 43 for how to enter BIOS Setup. As you boot up, hold down the "Del" key until the opening screen of Setup is shown (p 46). Click on Hardware Monitor at bottom left to get to that screen - see p. 63. On that screen at top right click on the particular SYS_FAN header that you plug your Hub into. then at the left click on the PWM button to ensure that this header will send a PWM signal to the Hub. Now use the Esc key to get back to the Main Menu and then the F10 Key to get to the Exit Menu - see p. 56. There choose the SAVE and EXIT option to be sure the new setting is saved and the system reboots.