The configuration of the automatic Like/Comments in articles is done in the Social configuration area of JFBConnect. In each tab of "Content Plugin -Comments" and "Content Plugin - Like", there's an option for "Position" of where the Like or Comment box will show up. Set that to Bottom and it should do what you're looking for.
Hope that helps, and good luck!
Alex
Content - JFBCContent is puting itself on the top of the page
