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Only way I know is to do samplings of rankings over a spectrum of easy and difficult phrases and the like on different kinds of pages on your site... and to pay attention to traffic and referral stats.
There's no point, IMO, monitoring rankings of thousands of phrases.
My tip: use Google Analytics to track the keywords that people use to find your site. Then analyze them: how many pages they see, how many time they stay, bounce rate... etc and then optimize your site to rank high for them.