Google Webmaster Tools identifies keywords for your site, however, this has no connection with performance for those keywords. These listed keywords are site keywords (for the site overall) but SERPs (search engine result pages) return results for individual pages. It is a mistake to expect to perform well for keywords within this list because the list does not indicate performance (not all sites perform well for keywords found in GWT), but rather use it as a gauge to know what keywords Google recognizes for your site. Use Google Analytics to know how you are performing for any keyword.
As well, if your site is relatively new, it will take some months before any page will perform for the keywords recognized for that page. Also note that performance is on a page by page basis so your SEO efforts has to be focused on individual pages and less on the site overall.
If you want to start off with SEO, then I can recommend MarketSamurai. I use that and SEO PowerSuite which is not for beginners. MarketSamurai is somewhat affordable and really will help you get started. I also recommend reading MOZs http://moz.com/beginners-guide-to-seo Beginners Guide to SEO. It is a great jumping off point! And it is free.