The server (API, UI, etc) is one container. “Node” in that sentence is a host/computer which will be used to run your containers. Each node runs the Rancher agent, which is another container, and that does what the server says to to create/restart/etc containers.
The server container can be run on a host that is also running the agent, but there is no reason it has to.
You add hosts to a Rancher environment. If using Kubernetes/Mesos/Swarm it is then also automatically added as the appropriate concept in there (e.g. node in k8s).