Kach22i: Good instinct... our roof doesn't have ice & water shield, and that's definately part of the problem. My original plan was to put it over the entire "low pitch" area, then use a good quality asphalt shingle.
However, the peel & stick roofing I'm talking about is designed to be used standalone.
Bakor & GAF are the ones I've heard about the most.
http://www.can-save.ca/index.php?option=com_content&task=view&id=235&Itemid=202
http://www.gaf.com/Content/GAF/RES1/ROOF/RS_Liberty.html
Polyglass & Flintlastic also sell the same type of roofing.
And as for metal, it is an option I am considering for the steep pitch areas. They are the only parts you can actually see from street level, and I think a steel roof would look great there.