The social buttons shouldn't be an issue as those are just some HTML code and not connected to your App at all. For user integration, that's a bit more difficult as the 'other' site would need to be able to read from the Joomla user tables to get their profile info. That's outside of what JFBConnect is meant for, so I wouldn't be able to help there.
The Facebook App you created for JFBConnect / Joomla should be used on the other sites, if it's on the same domain, so that if you make Facebook API calls, you get the same user id for the other site that JFBConnect gets for your Joomla site. If you use different API keys, Facebook will return different user IDs for the same user as a security / privacy measure.
I hope that helps explain things a little, but if there's anything more I can help with, just let me know.
Thanks,
Alex