A couple of things...
Regarding phase setting, it has the possibility of making a big difference due to the way your room reflections work out.

Regarding sub level setting: I tend to have the receiver set to the midway point, rather than have it very low and having the sub cranked, even though that's what SVS tends to recommend. If I do crank the amp on the sub, I end up with a bit of hum. Personally, to me it makes more sense to raise the level of the receiver, since it then outputs a stronger signal compared to any noise you would get.

I would say the best way to calibrate the subwoofer is to get a computer program like, NCHTone (do a google search) and use it to generate frequencies from your computer to your receiver. This will let you plot a frequency response of the subwoofer+speakers in your room. By doing this in my friend's apartment, we found changing phase setting had a drastic effect on his overall freq response. Part of the problem with the test tone is that I believe it only outputs at one frequency. Also make sure to compensate for the ratshack meter at lower frequencies. Hopefully by plotting a chart like this, it will tell you whether there is a hole in your freq response or not.