If I understand your question correctly, no. When a user's logging in through Facebook, our JFBConnect Authentication plugin is called up to deck and verifies the Facebook user is a member of the site. If not, we create them a completely normal Joomla user (assuming your have "Full Joomla User" set, not Facebook user only, that's a little different).
Either way, we save the password to the com_users table and when anyone logs in using Joomla credentials, we pass that information to the com_user component to validate the user. JFBConnect doesn't interfere or change this interaction at all. We definitely don't keep any separate passwords for users.
Hope that helps explain how we work, but if you have any other questions, just let us know!