I've fluctuated in my use of software for reporting search engine rankings. I feel that, on one hand, they shift the focus from 'results' to monitoring and getting hung up on rankings. On the other hand, using a large base of keywords that I feel represent the spectrum of what the site is optimizing for can some times provide some objective metric for determining the general direction your efforts are going.
I think you have hit the nail on the head, it's easy to get hung up on keyword rankings. There are many more important measures and I would recommend you read this outstanding book "Web Analytics: An Hour A Day by Avinash Kaushik". You can read a review here http://www.seo-blog.com/web-analytics.php
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