Here's how I recommend, and why.
The multi-headed cable from the PUMP unit of that Kraken X53 system has no outputs to the system fans. The rad fans are to be connected to a mobo fan header dedicated to the CPU cooling system. Although the system manual does not say so, I would hope it included a Splitter to use to connect both fans to a single mobo header.
The Pump unit gets all its power directly from the PSU via a SATA power output from the PSU that plugs into the wide connector on the multi-head. It is intended to run at full speed all the time, and that power source will provide the constant 12 VDC required. There's also a cable to be connected between a USB connector on the pump multi-head cable and a mobo USB2 header. This allows the NZXT CAM software utility to communicate with the Kraken X53 system.
The mobo CPU_FAN header has an important secondary function. It monitors the speed of the CPU cooling "fan" to be sure it is working. If its speed signal fails, the system will put up a prompt warning and, in a short time, likely will completely shut down your system even without waiting for the CPU temperature sensor to show a high temp. This is to protect the expensive CPU ship from damage from a rapid temperature rise with no cooling. When you use a AIO system like the Kraken, the speed signal that needs to be monitored for failure like this is the PUMP speed. No pumping and the temperature can rise rapidly. But if one (or even both) rad fans fail, the CPU internal temp will rise more slowly, and the normal temperature sensor and limiting system will protect the CPU. So, take the 3-hole connector from the PUMP's multi-head and plug that into the CPU_FAN header. It really only supplies the pump speed signal there - it does NOT get power or pump speed control from that header. Then take the connection for the two RAD FANS and plug them into the CPU_OPT header. It is designed to automatically adjust the speed of the CPU cooling device (in this case, the rad fans) according to the internal temperature of the CPU chip, and that's what the Kraken X53 design wants.
Get the mobo BIOS manual, see p. 10. Choose the CPU Fan. At upper right set it to use PWM Mode for the 4-pin fans on the rad. At bottom left choose the Standard Profile to use the pre-set automatic fan control system. Click on Apply at the bottom. Then Exit to get to Main Menu (p. 14). There click Exit at upper right to get to Exit Menu (p. 64) and choose Save Changes and Reset to save your settings and reboot. These settings will also be used for the CPU_OPT header you have connected your rad fans to.