Andy,
If JComments isn't using a content plugin to render the comments, then you'd need to do a bit more work to switch the ordering. Mainly, you'd need to disable the FB comments that are automatically be inserted and either add the JFBCComments module to the bottom of the articles/menu items where you want it to display or modify the Joomla Article template and add the {JFBCComments} tag where you want the comments to go.
The Joomla plugin system is very powerful, but if JComments are being added 'outside' of that plugin group, then you'd need to do the same thing.
Hope that helps explain, but if you need more help, we'll do what we can. I'm not familiar with JComments though, just so you know.
Thanks,
Alex