Ramon,
What popup, in particular? The actual authentication popup where it asks for the user's email and password for Facebook, or the popup saying "You are now being logged in with your Facebook credentials"? The first one is difficult to get rid of as we need to authenticate the user somehow. The latter popup can be disabled in the JFBConnect configuration area.
Let me know if that helps, or what you're looking to do, and we'll help how we can.
Thanks,
Alex