This chapter shows some general best practices for keeping your template.php file clean as well as making it easier for designers to work primarily with the template files when possible to avoid them having to make too many changes to template.php. Specifically, some HTML classes are removed from the ninesixtyrobots_comment_form() function in template.php and moved to the comment-form.tpl.php template file, which is specified as an option in the ninesixtyrobots_theme() function. The rendering logic is also removed from the theme function and into a preprocess function so that it can be passed in as a variable to the new template file.
Check your version
This video covers a topic in Drupal 7 which may or may not be the version you're using. We're keeping this tutorial online as a courtesy to users of Drupal 7, but we consider it archived.