Search engine optimisation is the art of getting your site ranked for the most appropriate terms in the search engines.
If your site is in a frame set it can cause problems for the search engines, they may not be able to read the page as a whole, this is because the page in a frame set is not one whole page but rather 2 or more depending on the design.
If you have your site set so that the top of the page and the navigation is in a frame and does not change then that is counted as one page and when the text and body of the page is displayed then this is another page.
So when the search engine tries to load your page all it sees is the outer navigation page that does not contain any body text and there are no keywords for the search engines to rank your site for.
You can get a similar feel to your site by using CSS to build the site rather than a frame and this will stop the problems of your site not getting indexed in the search engines.