I'm having a hard time figuring out what these two views show me.
Traffic Source->Sources->Search->Organic seems to show the key word a person searched for in a search engine, like Google.
What does Traffic Source ->Search Engine Optimzation -> Queries show? Are those search terms from within my site's search function, or are they also search terms from Google, etc.?
Traffic Source->Sources->Search->Organic shows data from all search engines - or, more technically, it shows visits from users who visited your website and ran the Google Analytics javascript while reporting a referer URL that Google interpreted to be from a search engine, including its own but also many others. Some of these hits from Google have the words not provided because Google has decided not to send the search terms in its referer URL to your site.
Traffic Source ->Search Engine Optimzation -> Queries shows selected data from Google Webmaster Tools if you have connected it to your Google Analytics account. This is only data from Google searches - or, more technically, it shows search results directly from Google's servers. Unlike Analytics, the data doesn't go back very far, is only an estimate, and cannot be analyzed with other Analytic data like browser, device, etc. However, it does show all Google terms, including the not provided ones, and since it comes from Google's search data instead of your website hits, it may also include results from users who block javascript/GA in their browser. It also shows ranking positions, impressions, and CTR (click-through rates), which can tell you something about searchers who do not visit your site at all.
