Thanks for the details. Now I can give more complete advice.
Your mobo is very well equipped for what you want, but there are still limits on the graphics cards.
Let's start with the CPU cooling system. It will consist of the EK-XRES 100 Revo D5 PWM attached to the Evo Supremacy block from EKWB on your CPU, and to some radiator system you have not specified, but that's OK. The pump unit is PWM style, but your rad fans will be 3-pin style. You need a control system for that, and your mobo has all you need to do that.
You can connect the pump unit's cable that ends in a female fan connector to your mobo's W_PUMP header (see manual p. 1-42), and its other cable that ends in a male 4-pin Molex connector to a female Molex power output from the PSU. This provides power to the pump from the PSU (it needs more than a mobo header alone can provide), but control of the pump speed will be by the mobo via the PWM signal coming from the W_PUMP header, and speed of that pump will be reported to the mobo via that same header.
You then connect one of the Phanteks PWM Hub units to the mobo CPU_FAN header via the Hub's fan cable, and to a SATA power output from the PSU via the Hub's other cable. Then the four 3-pin fans mounted on the CPU rad will plug into ports of the Hub, ensuring that one of those is plugged into the white Hub Port #1 so its speed can be forwarded to the mobo CPU_FAN port. This allows the mobo to control the speed of the rad 3-pin fans and to monitor the speed of one of them to be sure it is operating.
Finally for this system, you will need to adjust BIOS Setup configurations for these two headers you are using. See your manual on p. 3-38, "CPU Q-Fan Control [Auto]". Set this to PWM Mode to ensure that the header sends out the PWM signal that your Hub will need. Next page for "CPU Fan Profile [Standard]", just check that it is set to "Standard" (the default) so the mobo will apply its automatic control system to this fan header and control your CPU rad fans via the Hub. Skip down to p. 3-42, "Water Pump Control" and set that to "PWM Mode" so the proper type of automatic control signals will be sent to the pump unit. Next you have to set up three points along the pump's speed control curve. Unlike most temperature control systems, the mobo really can't know by default the right settings for all liquid cooling systems, so you will have to create initial settings and later experiment to discover the "optimal" ones for your pump. Think of these three points as part of a graph of pump speeds versus the CPU's internal temperature. Now, "pump speed" here is really set as the "Duty Cycle" or ("% On") of the PWM signal. So for each of Max temp, Middle temp and Min temp, you will set what temperature that is, and what Duty Cycle you want the pump to run when that temperature is reached. Whatever Duty cycle you set for the Max temp, that same will be used for any temperature above that. Similarly, the Duty Cycle you set for Min temp will be used for temps below that. I'd suggest 100% Duty Cycle for Max temp (whatever temp you choose), and about 25% Duty Cycle for Min temp. To choose those temperatures (especially the Max temp), check the chip maker's spec for operating temperatures of the chip. When you have all those settings made, click on the "Exit" choice in the top menu list and on the Exit Menu page (manual p. 3-53), click on "Save Changes & Reset" to save your new settings. This configuration and physical connections will provide power and automatic speed control (by the mobo headers) both to your pump and to your four 3-pin fans mounted on the CPU cooler rad.
Next, case ventilation fans, which are easy. You plan to use four 3-pin fans for this. Your mobo has four CHA_FAN headers, and each of them can be configured to operate either in PWM Mode or in DC Mode - the latter is what you need for your fans. But you want to reserve at least one of those headers for your GPU cooling. (That is difficult (below), but I'll still assume one needs to be reserved). You could connect all four fans to one header only by using a Phnateks PWM Hub, but that's not necessary. You can just as easily connect four fans to one (or two) of these headers by using simple splitters that are much cheaper, because the total load for four of those fans certainly fits within the limits of one fan header. For two fans each to two headers, buy two Splitters with two output arms each, like these:
http://www.newegg.com/Product/Produ...168&cm_re=fan_splitter-_-12-423-168-_-Product
Used this way, you will have separate control of each fan pair (although likely you will use exactly the same control settings, anyway), and the speed of ONE fan of each pair will be reported through the mobo headers.
To run all four fans off one header, buy three such splitters and "stack" them. That is, plug two of them into the output arms of the third; the result is a Splitter that converts one mobo header into four outputs. Then all four will be under the same control, and only one of them will have its speed reported. If you use Splitters (either way), configure the header(s) you use in BIOS Setup this way. Go to manual p. 3-39 and check that "Chassis Fan 1-4 Q-Fan Control" is set to DC Mode for each header used. If you have to change it, remember to go through the Exit Menu and select "Save Changes & Reset".
To run all four off one header but using a Phanteks PWM Hub, connect the Hub to one header and to a PSU SATA power output, and plug the fans into Hub port, ensuring one fan is in White Port #1. Now configure the header in BIOS Setup differently - this time it must be set to PWM Mode so that the Hub gets the PWM signal it needs. Then remember to go through the Exit Menu and select "Save Changes & Reset".
Now the hard part for which I have no complete solutions - your plans for GPU cooling. It appears that involves one more EK-XRES 100 Revo D5 PWM pump, two EVGA GeForce GTX 1080 FTW cards in SLI, two unspecified rads and six 3-pin fans. To do this you plan to modify both video cards by removing their supplied cooling fans and replacing them with unspecified water blocks (likely invalidating the warranties). I am supposing that you plan to connect the two water blocks in series and the radiators in series using the single pump. But maybe you have a parallel arrangement intended - I don't know, but that does not matter for control purposes. To power the fans and to allow control of their speeds is straightforward in part of the design. You can do all of that using one Phanteks PWM Hub for the six fans. The units you linked from ModMyToys won't do it. The first item is just a way to connect many fans to one power source and is fed by a PSU 4-pin Molex FEMALE connector. The second item is an adapter cable that ends in a Molex MALE connector, so it won't fit into the first. (The second item is intended for use with a distribution PCB similar to the one you linked, but with an input connector of the 3-pin fan type. That adapter can power such a PCB from an PSU FEMALE Molex output. But the adapter can't connect from a mobo male fan header to a PCB with a MALE input Molex.)
BUT you need to have a PWM control signal to that Hub, and some control system that adjusts that signal according to the needs of the two cards. Your hope to do that control currently rests with Speedfan, but I am not at all sure you can get that to work. Speedfan is a software utility that works with the hardware on the mobo to take over the control mechanisms for fans. Its advantages over the mobo's built-in control systems are that it offers somewhat more flexible control strategies, and it offers access to and use of more inputs from temperature sensors. I don't know if you want the greater control strategies option, but you are counting on access to temperature sensors from your GPU cards on which to base control of their cooling systems. From the info on the Speedfan website I cannot tell whether that is possible. It is clear that it claims to know how to access temperature readings from lots of hardware units but NOT all, so you would have to contact them directly to verify for sure that it CAN read (and read correctly!) the temperatures on each GPU card you plan to use. MAYBE the card maker, EVGA, can help on that point, I don't know. But I would NOT bet on getting a "Yes" answer without taking to them directly and specifically about those cards. IF you are sure that Speedfan will do this for you, then you might be able to co-opt one of the mobo CHA_FAN headers to do your control for you, by having Speedfan force that control loop to use the GPU card temperature as its control basis.
Don't get hung up on Speed fan using Voltage Control Mode. Speedfan does not change how a mobo header puts out fan control signals - it only uses what the mobo headers can do. As it happens, your mobo's CHA_FAN headers can be configured for either type of control. So IF Speedfan can make this work, you should plan to use that CHA_FAN header in PWM Mode to control a Phanteks PWM Hub, and then connect all six GPU rad fans to that Hub.
Now, if you cannot be sure that Speedfan can access and use the temperature sensors in the GPU card(s), MAYBE there is a way to steal some info from the cards themselves. This depends entirely on how those cards control their own fans in the original configuration. IF it exercises control of its own fans using Voltage Control Mode, you're out of luck! There is no product I know of on the market to snag a Voltage Control signal (that is, a voltage signal ranging from 5 to 12 VDC intended to power a fan) and use it to create a new set of six (or more) fan ports for 3-pin fans using Voltage Control Mode, and with enough power to handle those six fans. IF the GPU cards use that fan type, my guess is that the power each card has available for the fans it comes with might not be enough to run six of your chosen fans. (Well, maybe stretching a little, even powering three fans from each card with custom wiring.) HOWEVER, IF the GPU cards from EVGA actually use PWM fan types, then EVGA might tell you where to tap into the PWM signal on a card. Then you could mod the card to get that signal and take it out to the PWM signal input pin on a Phanteks PWM Hub, and let the Hub power and control your six fans for the GPU rads. That's a lot of "if's" and figuring out to do.
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