They're just the same as the distinctions made in English:
Einstellungen = Settings: General functions that alter the way the program operates.
Optionen = Options: Used to refer to theThe range of choices you have within an individual setting (e.g. black and white, colour, sepia), though not necessarily.
Konfiguration = Configuration: Often used to refer to settings chosen during installation that alter the way the program operates, or determine what parts of the program are installed, though not necessarily.