I still have comments showing up in two places--regular Blogger comments and Haloscan comments. I still don't know why this is happening, but I think I know how it's happening.
(Someone asked why I used Haloscan comments. It's because Blogger comments don't always show me everyone's email addresses, while Haloscan does.)
If you read my blog through a blog reader, you probably just click on the post title to read the whole thing. When you only look at one post at a time, the Blogger comments, and ability to post a comment through Blogger, are automatically included at the bottom of the page.
However, if you go to my blog through a bookmark or some other way that gets you to the whole blog (where you see several posts at once), you don't see the comments automatically, but you do see the Comments link. This link takes you to Haloscan comments.
Before I had to reload my template, all my comments went through Haloscan. With the "new" template, I had to also reapply Haloscan comments, and obviously something went wrong. I messed with my template for a while this afternoon, but all I managed to do is make several posts overlap each other.
If you want to see what everyone has said on a post, you might want to go to the "full blog" view (not just the latest post). If you click on Comments at the bottom of the post, you'll see Haloscan comments. If you click on the time at the bottom of the post, you'll see Blogger comments.