Yes, this will work. The Phanteks PWM Hub is different from other 4-pin fan Hubs in a way that is important to you. It REQUIRES a PWM signal to do its job, but then it uses that internally to create its own group of six 3-pin fan ports that use Voltage Control Mode (aka DC Mode) to control its fans. This method is the ONLY way to control 3-pin fans. But it also works fine for 4-pin fans because of a backwards compatibility feature in the design of 4-pin fans. For a 4-pin unit, this is not perfectly ideal, but it works very well, so you can use any mix of 3- and 4-pin fans on that Hub's ports.
Just be SURE to plug one fan into the Hub's white Port #1. That is the only port on the Hub that will send its speed signal back to the mobo header. If there is no fan on that port, the mobo header will believe that the fan plugged into it has failed and send out warnings.
The instructions for the Hub tell you to plug it into the CPU_FAN header, and then plug the actual CPU cooler system into the Hub's white Port #1. You do NOT need to do this. That advice is given only because there are many mobos now that use 4-pin CHA_FAN headers on the mobo but actually operate them as 3-pin headers that fail to provide the PWM signal. However, your mobo DOES provide that signal the Hub needs. So, plug your CPU cooling system into the CPU_FAN header directly. (See below for more). Plug the cable from the Hub that ends in a 4-pin female fan connector into one of the mobo's CHA_FAN headers. Connect a cable from the Hub to a SATA power output connector from the PSU. Then plug all your case ventilation fans into the Hub's ports, ensuring one of them is on Port #1.
To be sure this will work, check a setting in BIOS Setup. See your mobo manual on p. 3-7 where the fan headers are configured. Select the header you have used for the Hub connection and verify that, at top right, it is set to use PWM Mode. IF you have to change that, remember to SAVE and EXIT out of BIOS Setup.
Regarding the H100i V2 installation, follow its instructions. The fans on its radiator need to be plugged into the two connectors on the end of a cable coming from the pump unit. A cable needs to be connected from a socket on the pump to a mobo USB2 header. There is a cable from the pump unit that plugs into the mobo CPU_FAN header. Finally, you need to download and install the free utility from Corsair, Corsair Link. This utility takes over control of the H100i system to control the CPU cooling, and uses that cable from the USB2 header to communicate its orders to the pump unit and its fans. The utility MAY also give you a way to check and control the case ventilation fans connected to the Hub.
If you don't use the Corsair Link utility for case vent fan control, that Fan Xpert 4 utility that comes with the mobo (on its CD) will do it nicely. It runs under Windows so you can examine and adjust the fan systems. I advise you NOT to use it for CPU cooling control - let Corsair Link do that job.
With this set-up you can monitor and control all your case ventilation fans, whether 3- or 4-pin, through the included Hub. You should be aware, however, of a normal limit on such systems. A mobo header can accept a speed signal for display from only ONE fan. So any proper Hub or Splitter will send to its mobo header only ONE fan's speed signal, and all the other fans on the hub will have their speed signals ignored entirely - you will never see them.