I'm in the process of editing a theme for my website, and so far I have created all the themes in the themes directory, and Chmod'd them to 666 so that I could edit them through the AdminCP, BUT only some of the files are editable. One file that I noted that I couldn't edit was header.php
It didn't appear down the right hand side of the theme editor in the AdminCP, and when I changed the URL so that I had entered header.php, it said that the file was "Sorry, that file cannot be edited." But when I attempt to edit header.php in the Kubrick theme, header.php is editable.
Other files that can't be edited through the Admin CP are sidebar.php & footer.php