Creating a downstream cluster which is HA is adding nodes with the correct roles to the cluster. Automating this is interacting with the API to create the cluster (basically what is sent when you create it in the UI), and then creating the command to run on each node (with the correct role). Our vagrant quickstart has scripts for this (https://github.com/rancher/quickstart/tree/master/vagrant) or the other providers have Terraform examples.
If you want to do it using RKE, you can create a cluster to import and then run the kubectl command with kubeconfig pointing to your cluster. You will lose the ability to fully manage this cluster in Rancher as Imported clusters don’t get the same option to manage as a cluster created in Rancher. How to automate importing clusters is shown in http://forums.rancher.com/t/programmatically-import-cluster-no-web-ui/