With 2 fans on a y adapter your motherboard will only see one fan that's normal. Also I don't use the CPU fan header at all. I have the pump plugged into the PWR_FAN header and the two radiator fans on a y connector plugged into one of the OPT_FAN headers.
With the other fan headers can voltage can vary depending on your bios settings but the PWR_FAN header supplies 12vdc all the time which is what you need for your pump. You then need to go into bios - Advanced tab - hardware monitor - fan speed monitor and turn off monitoring for your unused CPU header so that warning will stop!
You then go to the Power tab - Fan speed control and Disable Cpu fan control and make sure the optional fan number that your using is not set to silent mode. All this is assuming that your bios is similar to mine.
P.S. With 1.36875v @ 4.4GHz and a Corsair H70 my idle temps are 28-32c @ 70f (21c) room temp yours should be even lower depending on your computer rooms temperature.