1) There's a few options here:
If not already logged into Joomla:
* You can enable the "Automatically Link Users by Email" setting. When a user tries to login with Facebook, if their Facebook email is already associated with a Joomla user, the accounts will automatically be updated.
* Alternatively, if that's disabled, they can be brought to the Login/Register screen of JFBConnect where they can enter their current Joomla credentials and connect accounts that way.
If already logged in:
* When you use the SCLogin module, a "Login With Facebook" button will show to users who are logged in, but haven't connected their Facebook accounts.
* You can add the following link anywhere on JomSocial for registered users to link accounts. When clicked (if they are logged in) it will map their Facebook user to the current account:
<a href="javascript:void(0)" onclick="jfbc.login.login_custom();">Link account to Facebook</a>
2) There's 2 main spots that the mapping of accounts happens for existing users. If you let me know which steps above you're using, we can gladly point you in the right direction.
3) That depends.. what is your Registration Flow setting in JFBConnect? Both would be in the /components/com_jfbconnect/controllers/loginregister.php file. For users that fill out the form, they are created in the createNewUser function. For users that have accounts auto-created, it'd be in the createFacebookOnlyUser function.
Hope that helps, but feel free to bounce back any other questions you have!
Alex