It depends on how you have set WP up. Check out the Template Hierarchy to see how WP picks the correct file.
Essentially WP does call index.php in the root, it then works out which of your templates to show from there using all sorts of logic and checking all sorts of settings and what not, including the aforementioned template hierarchy.
I wouldn't advise changing your .htaccess file as WP takes care of that for you and changing it can really screw your site up (re saving your Permakink Structure will fix it if it is broken).
GoDaddy or no, the host you are using really makes no difference.