Google Analytics and Google Webmaster Tools serve two purposes that are very distinct but also related: Google Analytics shows how human visitors interact with your site, and Google Webmaster Tools shows how the Google search engine crawler (also known as “Googlebot”) spiders your site and also how Google search engine users interact with occurrences of your site within the search results.
By associating your Google Analytics Web property (on the Property Settings tab) with your Google Webmaster Tools account, you can view Google search engine data, such as impression and clickthrough rate, directly in the Search Engine Optimization reports within Google Analytics.
How do the Search Engine Optimization reports differ from the Search > Organic report? For one, the Search Engine Optimization reports relate only to the Google search engine (and not to Bing, etc.) More importantly, Search Engine Optimization indicates how well your site and your listings are performing directly on the search engine, while the Search > Organic report indicates the keywords that are driving traffic but does not provide any context within the search engine itself.
For example, Search > Organic could indicate that your site is receiving 1000 monthly visits for each of two keywords, but a low average position or a low clickthrough rate for one of the keywords in the Search Engine Optimization > Queries report could signal an opportunity to optimize your site to achieve better search engine performance for that keyword.
For more information, see Using the SEO Reports in Google Analytics help.