You can do it -> https://github.com/docker/dockercloud-cli#namespace
Either you set the environment variable to work with your organisation or you prefix the env var before every CLI command, whatever works best for your use case.
Basically (maybe this info is useful to your automation), what CLI does is to add the namespace in the resource URI that you are going to work with. For example, the list URL to work with stacks is
Where the namespace is optional. If you do not specify the namespace, by default it will take the namespace of the user that logs in.
You can play with it with curl:
curl -u username:password https://cloud.docker.com/api/app/v1/stack/ will work in “username”'s namespace, but if you specify it, like in curl -u username:password https://cloud.docker.com/api/app/v1/myorg/stack/ will work in “myorg” namespace.
https://cloud.docker.com/api/app/v1/username/stack/ will work too, in username’s namespace. CLI adds this variable when you specify DOCKERCLOUD_NAMESPACE
Hope it helps. If you need anything else, do not hesitate to ask.