Do I enter my login name?
The name you enter into the settings dialog should be the name of the user on RuneTracker that you want to update the statistics of. This should be your display name, not necessarily your login name.
Does the updater start automatically?
The updater does not automatically start with your OS. To make the updater start with Windows, create a shortcut to the jar file inside your Startup directory (Start > Programs > Startup).
Where are my settings stored?
The updater stores user settings in %userprofile%\.runetracker-updaterrc. You can use this file to copy your settings between computers or simply to view the data stored by the program.