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If you added a new website in IIS, then the agent should automatically find it and add it in the controller as a new node the next time it starts up. Here are a few things to check:
1. Have you restarted IIS since you added the website?
2. Have you visited the website in a browser in order to get some calls to IIS and provide the agent with something to track?
3. Is there anything of note in the agent logs?
4. Are there any errors or warnings in Windows Event Viewer?