I haven't personally used the Scythe Kaze Master Pro Fan Controller, but have used the NZXT Sentry LX which has both fan speed control and temperature monitoring. Looking at the specs for Scythe Kaze Master Pro, there is no need to plug it into the mobo, but then why would you want to?
You can plug up to 6 (3-pin) fans directly into the controller, 6 temperature sensors, and 4-pin to molex that goes into your power supply. Once you connect all those up, you are good to go, independent of anything else.
Which is better to use the motherboard, or added hardware? My ASUS came with a controller an alarm, but to use my STW fan controller I need to unplug the CPU fan from motherboard and attach it to STW fan controller.
I am worried that the STW will fail and the my CPU will overheat