rel=canonical

will rel=canonical deindex your page? Can I make rel=canonical url get higher then the main url and be safe for google with this tag?

I am currently working on the seo report of a site, and the SEOMOZ report states the non appropriate Use of Rel Canonical tags. I did a google search and soon realized that this can make a huge difference in my ranks, but I can not figure out which URL is faulty and where the faulty URL...