I am under the understanding that pages that are in the root directory are the pages that are effective for SEO. But when I run a sitemap on a site that I used RSD on that has over 75 pages I see some but not all of the subsite pages. I am concerned as I have a project that is 350 pages and want to make sure that I get full advantage of such a large site. They have to be properly optimized and set up correct of course but want to get this right from the beginning so I dont have to redo later.

If a page is seen by the sitemap (if its not in the root) is it crawled and seen for SEO purposes?

Anybody have any input on this?