You can launch a server on the remote host by using the startrdodaemon script. This is the most common approach and it launches the server via a daemon process. With this script you are able to specify the port number to be used.
If you want to launch a remote server which does not use the daemon process, you can configure a new connection by using the startrdoserver script in the New Connection dialog in the Remote Systems perspective in the Eclipse IDE.
To ensure that your connection to the server recognises changes in your configuration - for example, changing the value of an environment variable - you need to disconnect and then reconnect to the server. You can do this by restarting Eclipse or by disconnecting and reconnecting using the Connection context menu within the Eclipse IDE.