You're correct that previously we only had 1 Facebook App. Facebook has changed their API over the last couple of years and split some features into 2 different types of apps, so it depends on the features you're looking to use.
Facebook (Consumer) - This is what most admins will want to setup. A consumer app is what allows users to authenticate, fetch their name, email, avatar and some other profile data. It also is used for social widgets like the Like button, Comments, LikeBox, etc.
If you had JFBConnect setup before v9, you should use the same API keys you had before in the 'Facebook' section (JFBConnect should automatically do this).
Facebook Business - This is almost exclusively for the Autoposting features to push your content to a Facebook Page or Group or pulling in a social stream from either of those to display on your site. Users will not be able to authenticate with this type of app and the 'Facebook' login button will not show if you only have a Business application configured in JFBConnect.
If you previously had Channels setup in JFBConnect v8, we recommend creating a new Facebook Business app and using those API keys in the Business section and then re-setting up your channels for auto-posting.
I hope that helps explain, but if you have any other questions, just let us know!
Thanks,
Alex