In docker you’d need to run something like docker exec -it <vikunja api container name> /app/vikunja/vikunja <vikunja subcommand> or with docker compose: docker-compose exec api /app/vikunja/vikunja <vikunja subcommand>
Since you’re running with docker, I’d suggest you to use env variables for the configuration of the container. For the time zone that would be setting an env variable VIKUNJA_SERVICE_TIMEZONE="Europe/Berlin" on the api container config. There should already be some configuration for the database if your config is based on the docker-compose examples from the docs.
After you’ve changed the config you will need to restart the container.
You could also add a config file which you would then need to mount at one of the config file locations into the container.
You only need to specify the config variables which are different from the defaults.
The default config is here, I’ve just pushed an update to the docs to fix the references.