Our JLinked extension automatically adds the 'in' overlay on the images. That's actually a requirement by LinkedIn.
For JFBConnect, the process should be pretty simple. In the /components/com_jfbconnect/libraries/facebook.php file, around line 185, you'll see:
$fql = "SELECT pic_big FROM profile WHERE id = " . $fbUserId;
Change 'pic_big' to 'pic_big_with_logo', and the image should be returned with the FB overlay.
I haven't tested this, but according to the FB documentation, that's all that's necessary. If you make the change, please let us know how it goes. I added a tracker issue for us to investigate adding an option like this to a future release.
Thanks,
Alex