The modal login is in SCLogin and you can do a template override for any of the files in /modules/mod_sclogin/tmpl/ directory. Login.php is the main file that will then load the other files as necessary. What files you need to override depend on what you want to add and where.
Likewise to override JFBConnect's login/register page (the page that a user is directed to when Automatic Registration is disabled), you will also need to do a template override of the /components/com_jfbconnect/views/loginregister/tmpl/default.php.
This should get you started, but let us know if you run into any difficulties.
-Melissa