The databases schema is kept up to date by Mendix. If you run your app locally, you can see this yourself. Run it first, stop it, change your domain model, run it again and you will be prompted to Synchronize your database. This will update your db schema with your new changes. You can even check what queries will be executed for this.
When running the Mendix model with a local build-in database, you can access the database via the Console option: use option Advanced and click 'Start build-in database viewer'.
There is no need for manual updates on the relations between tables, that is taken care of by the Mendix tooling.