The HTML Editor Extension just adds CKEditor to your site.
you can add custom plugins, but it will require editing the code.
The CKEditor files get installed to the webassist/ckeditor foldder.
follow the instruction from the plugin download for adding the new plugin to the plugins directory, then edit the HTML Editor code to add the new plugin to the toolbar array.
same for any custom skins, follow the CKEditor directions for adding the skin to the CKEditor install, then edit the code for HTML Editor to uuse the new skin.