You can use some application-specific features to do this, for example, for browsers you can use policies:
But not every application provides this functionality.
For a universal approach you can move the common application files to the template e.g. in /opt/app-data, create a script in your template that will move the files from /opt/app-data to the corresponding apps data location in app qube home directory and then create systemd service that will run this script on boot in the app qubes.