You should not use both at the same time. You should use the App ID you already created for CB. That will allow the users that have already authenticated your app to login without have to grant all of the permissions again.
As for if you'll run into issues, it's possible. JFBConnect won't know the 'mapping' of Facebook user's to Joomla users, and so therefore may try to either create the user a new account or send them to our Login / Register page. If you have the "Automatically link user's by email" option enabled, when a user logs in using JFBConnect, if their Joomla account has the same email address as their FB account, we'll simply create the mapping and everything should be normal though.
Finally, I'm not sure how JFBConnect and CB Facebook would cooperate if you continue using the authentication portion from CB and all the other features from JFBC. My guess is that there would be some conflicts as both extensions need to 'initialize' the Facebook Javascript and would do it in different (conflicting) ways.
So, if possible, disable the CB FB Connect. We can also look into migrating connections from CB's FB/Joomla user mapping table to our own. We already have an option to do something similar with JomSocial, but honestly haven't had the request yet for JFBC.
Hope that helps,
Alex
Community Builder and CB Facebook Connect Already In Use Question
