Part of the initial template used to create a Cloudera Manager instance or a cluster you can specify configuration overrides for all roles, services, management services or for Cloudera Manager itself.
As far as Director is concerned the list of services is static at this time and can't be changed during the lifetime of the cluster without creating a configuration drift that may make it impossible for Director to modify the cluster topology.
To modify configurations after cluster creation our expectation is that you will go and use the Cloudera Manager API directly. We are not planning to provide an API for that. Director will deny attempts to run cluster modify operations that change the list of initial configurations.