I have always preferred an embedded comment box over the pop-up, but I have had a problem with my readers not being able to read any of the comments beyond the 200th. This has been the case for both my previous and present templates. Using the pop-up box was not a good fix, since my readers still needed to click "Post a Comment" to trigger the pop-up just to read all of the comments.I finally found a fix today posted on Blogger Sentral. Although it took some trial and error because the language of my blog's template is a little different than what is shown in the tutorial, I was ultimately able to paginate my comments. If you are experiencing the same problem with your template, read the article "Solving 200+ Comments Display Problem" on Blogger Sentral.
Another great tutorial on the same site is "Numbering Comments in Blogger". There are many tutorials out there for numbering comments on Blogger blogs, but this one not only shows you how to number your comments, but it also explains how to make each subsequent page of comments not start over from #1.
