I don't know if the Preferences API is what you want. The way the preferences are stored using that API is platform-dependent. On Windows, it stores the preferences in the registry; that's hardly a place where you can easily edit them, and you can forget about editing them with Notepad.
The class java.util.Properties is part of J2SE. It's very easy to read and write configuration files using that class. Look it up in the API documentation.