The migration button will only check JomSocial for users that have already connected using JomSocial's built-in Facebook authentication and import those users into JFBConnect. All the users from JomSocial won't show up in the JFBConnect user-map area.. only those that had connected with Facebook using JomSocial.
So, my guess is that you have 200+ users in JomSocial but none (or not many) used the Facebook connect feature from JomSocial.
In that case, then you can just leave the "Automatically connect users by email address" setting enabled. Then, when users authenticate with any social network, if their email is already associated with a user in JomSocial, they're accounts will be linked and they can login immediately.
I hope that helps explain, but if you think there's still an issue, just let me know.
Thanks,
Alex