The module you're referring to is Phantek's PWM Hub. It is used to control may fans (any mix of 3- and 4-pin fans) from ONE mobo header. What is critical is that the mobo header be a real 4-pin port operating in PWM Mode.
Ideally, I say, you should do what you have done already - that is connect your CPU cooling system to the mobo's CPU_FAN port. Then you connect your case ventilation fans to one or more mobo SYS_FAN port(s). Now, Phanteks advises differently because they are aware (and warn you) of some odd circumstances in some mobos' SYS_FAN ports that prevent proper use of their Hub. One is that some mobo SYS_FAN ports can be set in BIOS SETUP to operate either in true PWM Mode or in true Voltage Control Mode. IF your mobo port is like this, it will work just fine as the Hub's connection, as long as you make SURE that the mode is set to PWM Mode so the hub can get the signal it requires. The other potential problem is that SOME mobos have 4-pin SYS_FAN ports that really are "cheating" somewhat because they are only 3-pin ports with a 4th useless pin, and they only operate in true Voltage Control Mode. Such a port cannot provide the PWM signal that the Hub requires and so it cannot work with this type of mobo port. To help you avoid both of these possible problems, Phanteks advises that you connect the single 4-pin female fan connector from its Hub to the CPU_FAN mobo port. This is because on modern mobos ALL CPU_FAN ports either are solely true 4-pin ports with a PWM signal, OR can be adjusted in BIOS Setup to operate in PWM Mode (default setting) or Voltage Control Mode. Thus you can always get a PWM singal from the CPU_FAN port, and that's why Phanteks recommends doing it this way. WHEN you follow their advice, it is the IMPORTANT that you connect your CPU cooling system to the one white Hub port #1. That is the only Hub port that will send back to the mobo fan port the fan speed signal it gets. Connecting this way sends the speed signal from the real CPU cooler fan to the mobo's CPU_FAN port, and that is necessary to let the mobo ensure the CPU cooling is working properly.
In my view, the ideal way is a little different. The "problem" I see with Phantek's recommendation is that it places ALL fans under control based on the temperature measured inside the CPU chip. Now, that's not terrible, since the temperatures of all mobo components are related to overall system workload, and that also is related to internal CPU temperature. BUT the mobo has a separate temperature control system based on a temperature measured by a different sensor built into the mobo itself. That is what was designed into the SYS_FAN ports. However, to use the Hub with one of these ports requires that you verify that the mobo SYS_FAN port you plan to use does, indeed, operate in true PWM Mode and provide a PWM signal to the Hub.
So, how would you do that? First, connect the fans this way, which is the "proper" way in my view:
1. CPU cooling system to the CPU_FAN port.
2. Phanteks PWM hub's 4-pin female fan connector to the chosen mobo SYS_FAN 4-pin port.
3. Phanteks Hub's power input cable connect to one SATA power output connector directly from the PSU.
4. All case ventilation fans connect to the Hub, ensuring that one fan is on Port #1 (white).
Next you MUST check the fan port settings and verify fan performance, as follows.
1. In BIOS setup, check the CPU_FAN port setting. Assuming you have a 4-pin fan for that function, ensure that the port is set to operate in PWM Mode and set to use automatic control.
2. Find the place to configure the chosen mobo SYS_FAN port. Set it to use automatic control. If you have a choice, set it to PWM Mode. If you have no choice, it is likely that it only operates in PWM Mode, and you'll be OK. But it might not operate that way, so do the performance tests to verify.
3. Start up the system and use it, trying to go from idling system to heavier use. Observe the CPU fan and the several case fans. Ideally, what should happen for BOTH groups is this: at the first moment of starting up they should go to full speed, and then drop back to slower speeds within a very few seconds. Later as you do heavier workloads the fans should all speed up. If you stop heavy work and let it just run at idle, the fans all should slow down.
If, instead, you find that the case ventilation fans all run at full speed all the time no matter what the workload is, that means the HUB is not receiving a PWM signal for the mobo port and cannot do its proper control. If you can't find a way to deliver the PWM signal to the Hub from a SYS_FAN port, you may have to follow Phanteks' original recommendation to connect everything to the CPU_FAN port.
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