Being used to override "Setting - default" defined values, "Setting - user" is just an empty json in both ST2 or ST3:
// Settings in here override those in "Default/Preferences.sublime-settings", and
// are overridden in turn by file type specific settings.
To edit the settings, just put the overrides in "Setting - user", let's say you want to change the default text size:
// Setting - default value
// Setting - user override
I was forgetting, you can access both Default or User files from Preferences' menu