We'd need a lot more details about what you're doing. How is the user authenticating if they aren't using JFBConnect? In general, we don't have any method silently authenticate them with just a token. We already have a Javascript call that can try to fetch their auth token and, if so, redirect them through the login process. That will reload the page though since that's what needs to happen when a user logs in.
Bottom line though, if you already know the user is logged in and the token is set properly in the Facebook Javascript library, you can call the jfbc.login.provider('facebook') call, which is what JFBConnect uses to authenticate all users.
I hope that helps explain,
Alex