There's a few ways to do this. We'd recommend you find a lightbox extension that can display a module in the pop-up. Things like RokBox work well, but there are plenty others. Then, you'll simply need to show the JFBCLogin module in this pop-up. JFBConnect doesn't do it natively, but hopefully the above will get you started.
Some modules, be aware, will require you to use a custom Login With Facebook button, instead of the default we use. That's because there can be Javascript conflicts between Facebook and the pop-up. A custom button will let you use any image, or text, for the button. You can read more about how to do that below, starting with the 2nd question:
www.sourcecoast.com/extensions/jfbconnec...on-support-questions
Hope this helps, but if not, or you have other questions, let us know!