There's 2 primary settings, and it depends on what you're going for for ease-of-use. The primary setting to play with is "Create New Users".
When set to yes, this will create a separate Joomla account that the user can log in with later. In this process, the user will be asked for their username, password, and email address. Upon returning to the site, they have the option of logging in with either their Facebook account, or the Joomla user they created.
Pros - More login flexibility, get to pick their own username
Cons - One extra page at login asking for information
Demo -
facebook.sourcecoast.com uses this method
When set to no, the user is created an account in Joomla that you can see in the admin area, but the user doesn't have access to this account. The username is automatically set for the user (the auto-generated username will be configurable in an upcoming release)
Pros - Quicker 'one-click' registration
Cons - Unable to set own username, unable to log in only as a Joomla user
Demo - This site
The setting can be changed at any time and will not affect users who already have accounts, just so you know. So you have flexibility to play.
Hope this helps. It may be a little confusing, but between the two options, you can choose what works best for your specific needs.