The index page isn't created using the template, so modifying the template won't cause the index.php page to be modified. If you wanted the template to be applied to the index page as well, you will have to apply that manually.
Your friends over here at WebAssist! These Dreamweaver extensions will assist you in building unlimited, custom websites.
These out-of-the-box solutions provide you proven, tested applications that can be up and running now. Build a store, a gallery, or a web-based email solution.