In general, the sitemap.xml is automatically generated. But you can manually override it in the Site Settings --> SEO/HTML --> Sitemap.xml Override area. If you want to override the automatic sitemap.xml, the contents you put in this area must be a valid site map XML format (http://www.sitemaps.org/protocol.html
After you clear out the "http://www.sitemaps.org/protocol.html", be sure to click save. Then you will want to clear site cache. You can read about how to do that here: Custom skin changes are taking too long to show up on my site?