Miamiman,
There are only limited controls that we can offer if you're using the JFBCContent plugin. The Social configuration will let you choose if the comment box appears at the top or bottom of the article. Then, in the Plugin manager, the ordering of the plugin will determine where it goes relative to other content plugins. So, if your comment extension is inserting the comments with a content plugin, if the JFBCContent plugin is ordered before the other plugin, the FB Comments will show first. If the JFBCContent plugin is ordered after the other plugin, the FB comments will show after.
That's the only flexibility we have with the content plugins though, and that's restricted by Joomla. If you want more flexibility, you'd need to modify the template of your article manager and manually insert the {JFBCComments} tag exactly where you want the comments to show.
Hope that helps,
Alex