--etcd-embedded=true flag, it will configure the embedded etcd server to listen the addresses specified by the --etcd-endpoints flag (http://localhost:2379 by default).
In the same host where Omni is running (in Docker, --network=host needs to be used), you can use the etcdctl command to back up the database:
snapshot.db file.
It is recommended to periodically (e.g. with a cron job) take snapshots and store them in a safe location, like an S3 bucket.
NOTE: When --etcd-embedded is set to false, the database is external and not managed by Omni. However, it still needs to be regularly backed up. For more info, see etcd disaster recovery.