Your mobo has several fan headers. For use with the Kraken X62 system, I suggest you connect the pump's 3-pin female fan connector to the CPU_FAN header, because that is where the CAM software will expect to find the pump information.
But that does get to a problem using the included fan hub. You are correct, the instructions imply that you must have a 4-pin fan of some sort connected to the Hub's white port #1. And I recall people posting stories in this forum saying it will not work without that. Now, there are two versions of how this could play out, depending on the details. First, it is vital that the HuB receive a PWM signal from a mobo header via its "PWM Cable". You can ensure that by plugging it into either of your mobo's CHA_FAN1 or 2 headers (Manual p. 1-17). Then in BIOS Setup (p. 3-7 to 3-9) choose the particular CHA_FAN header you have used and ensure it is set (upper right of the screen) to PWM, and at bottom to Standard operation. Then click on Apply and Exit. Then you plug NO fan into the white Port #1, OR a 4-pin fan (you don't have one now). If you use any 4-pin fan, it all should work just fine. If you plug into that header a 3-pin fan, it will always run full speed, OR it may not work at all. The unknown here is what the Hub will try to do with that header. If it does nothing fancy and sort of "assumes" that Port #1 is just to be treated as a 4-pin PWM fan port, it should work with NO fan plugged in there. BUT you might get an error message from the BIOS telling you the "CPU fan" (that is, the one attached to the Hub) or a case fan has failed because the Hub port is NOT receiving a speed signal with no fan there. If the Hub itself gets upset with no speed signal on that port and refuses to work, then all the Hub's fans will fail. In that case, plugging a 3-pin fan into that port may get the Hub to work, but it also may make that particular fan run at constant full speed.
There is another approach you can use with only the four 3-pin case fans supplied with the case. You simply do not install and connect that fan Hub. The case web page says it includes three 120mm FN V2 fans for the front, and one 140 mm FN V2 for the rear. Get a 3-output fan SPLITTER like this
https://www.newegg.com/Product/Product.aspx?Item=N82E16812423163&Description=coboc fan splitter&cm_re=coboc_fan_splitter--12-423-163--Product
Although it is a 4-pin model, it will work with 3-pin fans just fine. Use it to connect all three front fans to the CHA_FAN2 header near the front on your mobo. Then plug the rear fan into the CHA_FAN1 header near rear middle. For each of these two headers, configure them to use the DC Mode (manual p. 3-8) so they can control these 3-pin fans properly. The power requirements of those front fans (max 0.16 A each) mean that the CHA_FAN2 header (capacity up to 1.0 A total load) can handle three of them easily. This is the easiest way to deal with those four 3-pin fans supplied with the case and NOT use the included Hub with its attendant difficult requirements.
Last item, in case you need help on this. The case also includes a different Hub for its included RGB lighting strips. That hub also has a cable to connect it to a mobo plain RGB header, and your mobo has two. See your manual, p. 1-22. Do NOT try to use the Addressable RGB header (p. 1-23). This allows you to use the AURA SYNC software utility included with your mobo to power and control the RGB lighting effects of the case.