There are two steps required for getting the deployed application fully configured:
Gutenberg can be configured using environment variables, these can be set in a .env file in the root of the repository.
A list of these and their purposes can be found here.
If you are hosting this on fly.io, you can set these as secrets in the fly.io dashboard.
The institute specific templating is controlled via a yaml file in the config directory, this contains a yaml file for each institute, e.g. config/oxford.yaml for Oxford.
The details of what is controlled by this config file can be found here.