PWM Hub pump connection
CPU_FAN header is nothing special. Most cooling products recommend you to connect their stuff to the CPU_FAN header so that the cooling solution can respond to the changes in CPU temperature.
Also, voltage regulated fans/pump = 3pin. PWM regulated fans/pump = 4 pin.
Now going to your question, a quick Google search revealed that the fan connector that is coming off your pump is a 3 pin header. So a 3 pin header will run at full speed when connected to your motherboard CPU_FAN header regardless of the CPU temperatures, since the CPU_FAN header is a PWM header with 4 pins (the extra pin is the modulating one, which the pump header lacks, and thus runs in full speed all the time). So there is no benefit in connecting the pump to the motherboard, and rather you should connect the fan hub to that CPU_FAN header to control your PWM fans. The pump can be connected to any other header, or can be left out altogether, since there is a molex connection feeding power to it.
Just a sidenote, some ASUS motherboards also support controlling of voltage regulated fans/pumps (i.e. 3 pin fans/pumps), so then connecting the pump to the motherboard would make sense as you can control the pump.
Hope this helps.
EDIT: Isn't this your pump? : https://shop.ekwb.com/ek-d5-vario-laing-d5-vario
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