I'm currently using a Corsair H110i GT AIO cooler (waiting for my CLC 240 to arrive tomorrow), and I use CPU temp to control fan speed. I also used CPU temp to control fan speed on the three other custom loops I built back in the day.
 
The problem with using coolant temp to control fan speed is that the coolant temp lags waaaaay behind changes in CPU temp; when the CPU starts to heat up, it heats up *fast* and you want those fans to speed up quickly in response to the increased heat.
 
But as long as you are also monitoring your CPU temps and not having a problem using your current method, that's fine. But most AIO's and most all custom loops do measure cpu temp and not coolant temp to control the fans. It's really a bit odd that EVGA's software uses coolant temp for fan control.