For reference, I set the node path to this:
Preferences prefs = Preferences.userRoot().node("/Prefs");
I thought that this would store the preferences file in a folder called "Prefs" inside of the working directory for the application I'm developing, but that was not the case. Now I can't find a folder called "Prefs" in the user ~/Library folder or the system /Library folder. I am able to use this preferences object to store data and everything is working as normal.
TL; DR - I can't find where my preferences are being stored based on the given code.