Yeah, there unfortunately is one thing you need to do to be able to actually moderate the comments. In the Social configuration area of JFBConnect, click on the Open Graph tab and enable Open Graph integration. Then, in the big box for setting defaults, set your application ID as follows:
app_id=12345
Where 12345 is the Facebook Application ID of your app, which can be found in the Facebook API tab of the configuration area. In the upcoming 4.0 release, we'll be automatically setting this value, but for now, you need to manually set it up.
Once done, it may take a few hours for Facebook to register the application owner for your comments, but when it does, you'll see a "moderate" menu option under all comments that any administrators of your application can use.
Hope that helps, but if not, let us know!
Alex