Instructions for how to do this for version 0.11 can be found at the Trac site, here's an example from that page that adds custom CSS as well as a header and a footer.
  Say you want to add a link to a custom
  stylesheet, and then your own header
  and footer. Create a file
  /path/to/env/templates/site.html or
  /path/to/inherit/option/templates_dir/site.html,
  with contents like this:
<html xmlns="http://www.w3.org/1999/xhtml"
      xmlns:py="http://genshi.edgewall.org/"
      py:strip="">
  <!--! Add site-specific style sheet -->
  <head py:match="head" py:attrs="select('@*')">
    ${select('*')}
    <link rel="stylesheet" type="text/css"
          href="${href.chrome('site/style.css')}" />
  </head>
  <body py:match="body" py:attrs="select('@*')">
    <!--! Add site-specific header -->
    <div id="siteheader">
      <!--! Place your header content here... -->
    </div>
    ${select('*|text()')}
    <!--! Add site-specific footer -->
    <div id="sitefooter">
      <!--! Place your footer content here... -->
    </div>
  </body>
</html>