I just use the Facebook login button - https://developers.facebook.com/docs/reference/plugins/login/
Once the user has used that to login (if they weren't already) and grant access to your app (site), the PHP-SDK should have no trouble using the Facebook session and APIs.
I just tried this with the new version 3.0 PHP SDK and it is definitely not working. Found this on the developer blog
In other words, use the v2 PHP SDK until the JS SDK is updated.