Add your css and js
info (as below) into the <head> section of your master page if you want to apply the css and js
to all pages, or drop them into the head section of the default.aspx page if you only want them to apply to the Default.aspx page.
<link href="Styles.css" type="text/css" rel="Stylesheet" />
You can also drop them into the "head" ContentPlaceHolder if needed.