Peter,
If you have the "Automatically Link Users by Email :" and the user is logging in with Facebook or Google and that social network email is the same to an existing user in Joomla, the accounts will automatically be linked. If there is no matching email, then it depends on your registration mode.
* If set to "Regular Registration", the user will be brought to the Login / Register page where they can login with their existing account.
* If set to "Automatic Registration", a new user account will be created for the user. In this case, there's no way for JFBConnect to know that they user already has an account.
The SCLogin module also has a setting for "Show Connect Account Button(s)". That will show the FB or G+ login button when user's are logged in *if* they haven't connected to those accounts. That will allow the user to 'connect' their Joomla account to those social networks and login with them later.
I hope that helps explain,
Alex