Thanks for the kudos on JFBConnect, we always appreciate hearing it!
As for the Content plugin, you can configure the location of the Like and Comment button in the "Social" tab of JFBConnect. Just click on the "Content Plugin - Comments' or "Content Plugin - Likes" tab, and use the "Position" setting to move either to the bottom of the article.
No editing should be necessary. Hope this helps, and good luck!