Settings you send to the controller by clicking the disk icon will run w/o aquasuite. I do not think you need to start AS 2012 with windows. Shoggy or Sebastien can clarify this.
That's cool, so once it's set up it doesn't matter what's running, fan control would work even under Linux or at the BIOS screen? I did wonder exactly what that disk icon did. Hopefully Shoggy or Sebastien can confirm this.