Theme not over-riding old styles

I started out styling my site using a stylesheet within the root directory (as in usual websites – i.e. not using themes) and edited the index.php in the root directory accordingly to use this style sheet.

Now I’d like to start using the functionality of single.php and so need to use themes (I assume) but when I select a theme, even the default theme, the original style still shows.

Do I need to replace the index file so it’s as it was when first installed? Or am I doing something else wrong?