change directory where PhpStorm stores config and system directories ?

You can change PhpStorm config files directory editing by Idea.properties file which is available in your PhpStorm installation directory.

Can this option be applied on existing installation, or have I to reinstall the app?

You can do this with your existing app.

Move your existing PhpStorm config folder to your new desired directory than point new directory path into idea.properties file.

See https://www.jetbrains.com/help/phpstorm/tuning-the-ide.html#common-platform-properties for the full documentation on this

Another link: https://intellij-support.jetbrains.com/hc/en-us/articles/207240985