Zach,
Thanks for the complements on the Facebook integration.. yes, it's pretty robust, but we always have more in the works
1) How are you posting that article to Facebook? That will help us determine the best answer to your question. I'm assuming you're just sharing it to Facebook, and in that case, then, no, the comments for each would be separate. The reasoning is that, when you post a link to an article on Facebook, that post is not part of the article, it's more like a comment by itself on Facebook. Comments attached to the wall post are just that, comments on your post itself, not necessarily the article.
2) This isn't currently possible as Facebook doesn't have a way that we're aware of to have comments post right to a wall.
With that all said, we're currently planning and scoping out version 4.0 of JFBConnect. One of the features planned for this release is a way to show your Joomla site inside of your Facebook page. If all goes well, you should be able to use a separate template (to accomodate the shorter width page), but basically, your articles and site will display directly in your Fan Page well under one of the tabs. It's still be scoped out and implemented, so things may change, but we're very excited about the feature. While it will be a little basic at first, it should evolve nicely with some good ways to tie your site and Facebook much closer together.
In this case, an article on your site would actually show in Facebook, and any comments posted would be displayed on either site.
Hope that all helps, and if there's anything else we can help explain or help out with, just let us know!