The profile that is created is specific to the monitor. You shouldn't be making adjustments to your brightness and contrast via the video card, but rather the monitor. I use a hardware calibration system too. The sensor is hung in front of the monitor, and the software reads the monitor's colors and brightness range, and you adjust the monitor to make it fit within a set of specific standards. The profile that is generated is for that monitor. If you want to do a second monitor, you hang the sensor over the second monitor, and do the same thing, adjusting the settings on the second monitor to fall within the ranges as well.
Through your video card driver, you tell it which display should use which profile.