A while back, I adjusted the comments plugin locally so that it would allow me to have plugins that change the template type they use from "story" to other things. A couple of months ago, I sent Ted an email with which pieces go in which templates. Figured I'd stick that here in case someone is looking for it.
This is only for the "story" section. The head template goes before and the foot template goes after this example. This also only works with the latest version of the comments plugin that has the template stomping code removed.
<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> <-