I'm afraid that you also mix up CSS with template. Any theme consists of at least this index.php (in the theme's folder) AND the CSS file. Only together they function as a theme: the index.php is the architecture (or structure, if you will), the CSS file is what decides on the look and positioning.
The root index file should never be meddled with. If it isn't as in Moshu's sample, either you or someone else did so obviously not knowing what they were doing.
A common mistake is uploading a new theme, and placing the index.php of the theme not in the theme folder, but instead in the root folder.