Tracy,
This is Alex

Thanks for posting here. It's much easier to show your question to the right developer when posted here.
From what you've described, here's the best/easiest solution. This will make it so that -any- comment box is for logged in user's only. If you need something more selective (some boxes for logged in, others for both), let us know.
In the /plugins/system/jfbcsystem/jfbcsystem.php file. Around line 671, you'll see:
Change that to the following block:
The 2nd line there can be customized how you want (and I hope it's not too confusing. You can also set it to return "" to return nothing. Figured you'd like the output from the above though which will show the number of comments and try to solicit the user to login.
The above is untested, but pretty confident it should work. If you run into issues though, let us know!
Thanks,
Alex