I guess I did not make things clear enough, because I think you misunderstand somewhat. However, with the info you have provided I can be more specific.
You are correct to be concerned about exactly how your mobo would control the case ventilation fans separately from the CPU cooling system. Case fans should be connected to mobo SYS_FAN headers, because those are the ones whose control is based on the actual temperature of a sensor in the mobo. (The CPU_FAN header's control is based on temperature inside the CPU chip, based on a different sensor located in that chip.)
You should understand that very few third-party Fan Controllers can do anything like automatic control based on temperatures, because none of them have access to those mobo temperature sensors. Most only allow YOU to set a manual control for the speed of each fan, and that means you must decide what speed to set to get the right cooling. But the specific controller you are talking about, the original NZXT Grid, does not even do that. It is not really a fan control system at all. It is a wiring hub which allows you to connect all your fans to a central block rather than to mobo SYS_FAN headers, and it provides power for all its fans from a fixed 12VDC supply from a PSU output connector. This means that all those fans will run full speed all the time. Its instructions say that the only way to get any control of its fans is NOT to connect it to the PSU, Instead, you can connect it to ONE mobo SYS_FAN header that is using Voltage Control Mode, and then it can act just like a multi-output SPLITTER. The potential problem is that, unlike a PSU output line, the mob header has a limit of 1.0 amps total load for all the fans connected to it. For the specific Noctua fans you list, they each consume 0.2 amps max, so you should plan on connecting no more than four such fans to one SYS_FAN header. You can get exactly the same functionality from using splitters, BUT using them with your mobo's SYS_FAN headers can give you complete mobo-based automatic control.
Your mobo has three SYS_FAN headers with 4 pins on them, BUT the manual's diagram for them on p. 41 makes it clear that they all use only Voltage Control Mode, the system for 3-pin fans. Now, 4-pin fans also can be controlled well by such a system, although it is marginally not as good as true PWM control. But the key point here is that, given the SYS_FAN type you have, you can NOT use a 4-pin Fan HUB to connect multiple fans. A HUB requires a PWM signal your mobo's SYS_FAN headers cannot supply. However, you CAN use SPLITTERS to connect up to four of your fans to EACH of the three SYS_FAN headers you have. Even though the fans are 4-pin type, those headers using Voltage Control Mode will power and control them just fine.
A SPLITTER consists of one arm with a female (with holes) connector to plug into a mobo SYS_FAN header, and two or three output arms each with male connectors to plug into the fans. Of those outputs, only one will have all its pins - the other(s) will be missing Pin #3, and that is the proper design. A SPLITTER just connects all its fans in parallel to the header's output. A HUB, on the other hand, may look also like just a group of wires, but it has one extra arm that connects to a PSU power output. It gets all its fans' power from the PSU and hence is not subject to the current limit of a mobo header. HOWEVER, a HUB MUST have a PWM signal from the mobo header, and your mobo cannot do that, so you cannot use a HUB.
I'm not sure how many case fans you plan, or how you want to distribute them over the three SYS_FAN headers you have. When you shop for SPLITTERS, you may not find any of the older 3-pin style, but that's OK. 4-pin splitters work with both 3- and 4-pin headers and fans. Those usually available include ones with two or three output arms. If you need more outputs, "stacking" works: buy three two-output Splitters and plug two of them into the two outputs of the third splitter, and you make four outputs from one mobo header.
If you use splitters to connect all your case fans to mobo SYS_FAN headers, then all of those fans will be automatically controlled by the mobo. The control is based on the TEMPERATURE as measured by a sensor built into the mobo. It is TEMPERATURE that is the target for control, and the mobo simply alters the fans' speeds to ensure the measured temperature is maintained on target. You do not have to make any adjustment to achieve this.
Regarding your plans for the Corsair H115i cooling system, they do not correspond with how Corsair says to do things. Their instructions, I realize, are based on having only two fans on the radiator whereas you want four for push/pull. The instructions say that you connect the pump unit to a SATA power supply output from the PSU, and then connect a cable from the pump unit to one mobo CPU_FAN header. You then connect each of the radiator fans to sockets on the pump unit and NOT to mobo headers. Then you connect a communications cable between the pump unit and a mobo USB2 header. Finally, when you start up, you download and install their custom Corsair Link software. This software uses information from the CPU and mobo and communicates with the pump part of the cooling system to control the fan speeds on the radiator. It also is a display and control center which allows you to configure that system as you think best. If you want to add two fans to the radiator, I advise you check with Corsair about how to connect them. It MAY be permissible to use common fan splitters to connect two fans to each of the pump unit's output sockets, but I don't know that, so ASK Corsair for guidance. The thing to bear in mind is that Corsair designed this system to do its own fan control, and not to simply use the mobo's automatic fan control for the CPU.