OP asked for the preferences folder that stores NSUserDefaults. Check /var/mobile/Library/Preferences/ for that, assuming your app is running as mobile user.
(Documents folder is a different thing, and is located in /var/mobile/Documents)
Note that, starting from iOS 8, these plist are cached in memory in the cfprefsd daemon, so overwriting files in this folder will have no effect unless you kill this daemon.
See http://iphonedevwiki.net/index.php/Updating_extensions_for_iOS_8#Preference_saving for detail.