The Client Management server and the Portal Managed client capabilities run within the context of the platform, so have access to the APIs necessary to update preference values. If you are not using these built in capabilities, changing preference values is more difficult.
You can update the default preference values by changing the plugin_customization.ini file, but if you want to perform updates on the current values, you will need to call APIs to make the changes.
You can use install handlers to set initial default values, but if you need to query current values, or perhaps make updates to existing values, you will need to provide your own mechanism to call the APIs.
You can also use the Managed Settings provider infrastructure to implement your own preferences settings capabilities.
While the preferences values are stored in the file system on the local machine, it is not recommended that the files be changed outside of the APIs.
Parent topic: Managing using another management system: XPD622