From the standpoint of the motherboard the pump is treated exactly as if it were a cooling fan. If you have temperature sensor headers on your motherboard, you can use the temperature to control the pump. I can do this with FanXpert 2 on my Asus ROG motherboard. But I realize that it probably isn't very common.
But you could use a fan controller control panel with the temperature probes installed on your graphics card. Or you could simply attach the thermocouple to your reservoir.
I've not seen an inline thermocouple for use in water cooling. You could possibly fabricate one using a "T" connector.