The Skin Editor HTML screen lets you add code into HTML areas of the page.
See the http://www.w3schools.com/tags/tag_doctype.asp for more information on HTML doctypes.
The default doctype for Confluence 5, and the one used in the ThemeBuilder ROOT theme, is <!DOCTYPE html>. You can change this in a custom skin, but you should be aware that it will change how your pages are interpreted by the browser.
The HTML Tag option allows you to add attributes to the <HTML> tag for all pages viewed with the skin. The primary purpose of this option is to add a VML namespace when using things like Google Maps API.
Header - Body - Footer
Each of the Header, Body, and Footer sections has a popup editor that enables access to write additional HTML into the Header, Body, and Footer sections of the current skin.
You will need to click the Save button to apply any changes made in the HTML screen.