[Simon]

Maybe i haven't understood correctly one of the original questions, but you define which templates are used in the main files, for example:

In index.php, the final line is $main_smarty->display($the_template . '/index.tpl');

This is calling the index.tpl template file when index.php is used. So if you want to rename index.tpl to main.tpl for instance, you'd do so, and then change the corresponding line in index.php.