In reply to Joseph.

Joseph, from what I'm seeing on your site, I'm guessing that you aren't using the Semantic Linkbacks plugin. Doing so will add a parser so that comments, replies, likes, etc. look a bit better (ie more natural) in your comments section, and it'll also give you the ability to facepile each type selectively.

Additionally, with your Webmention piece set up, we ought to be able to carry on a site to site threaded conversation from our sites. Thus, instead of replying directly in my comments section, you should be able to go to my last reply on your site in your comments section and reply to that instead. Your site will then webmention mine and the comment will appear on my site as well. (Hopefully this makes sense.)