OK, here's my best suggestion for your situation. You want to power the Kraken M22 system (pump plus one radiator fan plus an additional radiator fan) to cool your CPU, and you also need to power and control the case fan(s). On the radiator, your plan is to mount the two fans in a push / pull arrangement. For this your mobo has only one CPU_FAN header and one SYS_FAN header.
For the CPU cooling system, the pump needs to have a constant 12 VDC power supply so it always runs full speed, and the two fans need to have power plus control of their speed based upon the internal temperature of the CPU chip. The fan needs can be met by the CPU_FAN header using the normal automatic control and suitable configuration of the CPU_FAN header. The pump needs also can be met through this header, although I suggest a particular way to connect them so there is no risk of overloading that header. Thus, all three of these items need to be connected to the single CPU_FAN header. I suggest a simple device like this
https://www.newegg.com/Product/Product.aspx?item=N82E16812423165
Although it looks like a collection of cables, this actually is a 4-pin fan HUB with four outputs. This Hub gets all power for the connected devices from the PSU directly, via a connection to a 4-pin Molex output connector which you say you have available. Thus it draws no power from the CPU_FAN header. It does use a standard female 4-pin fan connection to the CPU_FAN header to get the PWM control signal from there for use by the fans, and to return to it the speed signal of one of its connected devices. Like other Hubs, this Hub will return to the host header only ONE device's speed, and that is used by the mobo to monitor for failure of the critical cooling system component. For an AIO system like this, the PUMP is the critical part whose failure must be detected quickly if it ever does fail. (If both fans were to fail, the CPU temperature might rise slowly, but that would be detected by a different system that monitors the CPU's internal temperature and prevents overheating.) So, here's how to connect. Plug the Molex power connector and the female fan connector into the PSU output and the CPU_FAN headers, respectively. Look closely at the four output arms of the Hub. Only ONE of them will have all four pins in it, so use that one to plug in the fan connection cable from the PUMP. This will ensure that it is the Pump's speed signal that is fed to the CPU_FAN header for failure monitoring. Then plug the two radiator fan cables into two other Hub outputs, leaving one unused. Now in the mobo manual, see p. 25-26 to configure it in BIOS Setup. First make sure you have selected the CPU_FAN header. Set Fan Speed Control to Normal, Fan Use Temperature Input to the CPU sensor, not the mobo sensor (IF there's a choice), Fan Control Mode to PWM, Fan Fail Warning to Enabled. Remember to SAVE and EXIT to save your new settings.
Note two things about this arrangement. One is that the new added fan you buy and install on the rad must be of the PWM (4-pin) type, because that's what the original fan is and that is the type of control Mode this system is using. The other is that this arrangement can NOT "see" the actual speed signals of either of those rad fans, so from time to time it is up to you to check to be sure they both are still working. With this arrangement, both fans will be controlled by exactly the same signals and will operate the same, changing speeds as the workload varies.
The details of power to the pump are little confusing to me. The M22 manual says the "Pump Power Cable", which is shown in the drawings as having two wires to Pins 1 and 3, must plug into the CPU_FAN header or the PUMP header if you had one. If all that is correct, that would feed the pump speed signal to that header via the Speed and Ground lines, but there is no wire for +12 VDC power from header Pin #2. Now that may be an error - the drawing may be wrong and there really is a wire on the Pin #2 position to get 12 VDC to the pump. (Since the header is set to use PWM Mode for control, the power supply from Pin #2 will always be 12 VDC.) If not, then the only other connections to the pump unit apparently are via the cable from its side socket to a mobo USB2 port which could supply power at +5 VDC and Ground to the pump, so MAYBE that is how the pump is powered. Whatever is done, though, you DO need that USB2 connection so that the CAM software utility can control the system and monitor for failures.
All of this leaves the mobo's only SYS_FAN header available for use with your case ventilation fan(s). In BIOS Setup (manual p. 25-26), configure it by selecting the SYS_FAN header and setting its options to: Fan Speed Control to Normal, Fan Use Temperature Input to the Motherboard sensor, not the CPU internal sensor, Fan Control Mode to PWM IF the fan is 4-pin (set to Voltage if 3-pin) , Fan Fail Warning to Enabled. Again, remember to SAVE and EXIT to save your new settings.
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