Not sure modifying is right, but yes the php file. The tutorial I like, creates the files from scratch, but it is a bit older, so the comments.php is not current. Sure there is the modifying themes php files for clients, which is cool. Creating my own theme from scratch started as a learning project for myself, while two clients are already using the theme, so there is sells potential, I also want to finish learning the basic files. So I posted the question about a tutorial here.