Well, I don't have a Spyder3. But, with my old Spyder2, it's best to turn off the Ambient Light Check at the beginning of the process. For the first calibration, then, you can leave your Brightness and Contrast set to the default settings until the software tells you to do "something". But then, you may want/need to dial down the Brightness, and then you can run the calibration again.
Brightness is one of the more challenging things to "get right". Your typical monitor will start out way too bright and calibrating doesn't always get it right. So, do what "looks right" to you, but then you will need to do the "acid test": test prints from a reliable source will be needed (it's best if they provide you with a printer profile if you can "soft proof" in Photoshop, and make sure they don't do any "corrections") and then you will need to view the print(s) in good light, meaning something approaching daylight (not so much direct sun, but a good amount of light, and, for color, the light "temp" should be close to the temp of daylight).
Run through that process and, if needed, adjust the monitor brightness. Repeat if needed.
It's good to do this with a number of prints of various tonal values and a range of colors as well as at least one B&W print.
In my experience it can take a few tries, maybe a couple, maybe you will get it right with just one, but the end result is that you can then move on to do your post-processing and when needed, printing, with confidence.