This should explain which flavour templates are in charge of what using an example.
<div class="news"> <- story.html <h2>$title</h2> | <div class="content"> | ... | </div> | links | </div> <- <div class="comments"> <- comment-story.html <div class="comment"> <- comment.html Posted by $blah at $blah | $blah | </div> <- <div class="comment"> <- comment.html Posted by $blah at $blah | $blah | </div> <- <div class="commentform"> <- comment-form.html form stuff here. | </div> | </div> <-