I would save the template as a dynamic template using the extension .dwt.php
Only the main navigation will be added automatically. The menu editable region will be converted from a neditable region and the CSSMenu Writer menu will be added in its place.
The other editable regions on the page will have records created in the content management database.
You will need to edit the CMS content for the secondary and footer menus.
You are correct that a template is not created for the Index page. but you should be able to edit the layout, can you give a little more detail on the issue you are having with editing the index page layout?