Jim, I had an S1-iS for my viz system until it failed* and Canon sent an S5 to replace it. I believe that with both of these models, white balance is handled first by an adjustment within the camera, with further refinement through the software and monitor settings.
Check your Canon user's manual for instructions. As I recall, all I had to do was place a white sheet (matboard, it was) under the lens and push a button or two to calibrate the white balance. After you calibrate the camera, then fix the settings of your software and monitor.
Note that if you change your lighting set up, you may have to recalibrate white balance in the camera, and readjust the software and monitor. Any change of lighting, such as sunlight beaming through a window at certain times of the day, may cause inconsistent results.
At least, that's been my experience, and the several viz systems I have used have all been the same in that regard.
* Canon had a batch of defective chips that were used in S1 and other cameras. Canon has (had?) a web page about this issue and offered to replace cameras that failed, even beyond the warranty period. If your S1 ever gives up, maybe Canon will replace it free for you. Check this thread:
http://www.thegrumble.com/showthread.php?t=29084&highlight=defective+Canon