There is great value in connecting the two powerful, free tools from Google. Most importantly is ‘trend’ analysis: The art of eyeballing to see if something is going wrong. WebMaster Tools is accessible through Analytics removing the need to login to the two tools separately for this check. Of course, this assumes you are up on running on Google Analytics and Google Webmaster Tools and have these set up correctly.
The search query report will show you if search impressions have dropped off for major keywords. Look at the search queries report every few days (or weeks depending on urgency and obsessiveness levels) to get an idea of where you may be losing ground with search visibility.