Many settings, for example saved searches and virtual libraries, are stored in the database. If you aren't seeing changes to these preferences then the two clients are seeing different databases, probably because of conflicts. In other words you have already broken your library. If you haven't then there is a good chance you will, especially using Google Drive.
Putting the above aside, preferences that are stored per user are saved in the calibre configuration folder/directory, which is not in the library. Move this directory to the shared storage and use the environment variable
CALIBRE_CONFIG_DIRECTORY to point at it.