To set up SSL with automation in Cloud Manager, first login to Cloud Manager and navigate to the Deployment tab, where you can configure SSL settings by clicking on Authentication & SSL Settings. You will need to enter the path to your CA file, choose client certificate mode, specify a PEM key file for your Automation, Backup, and/or Monitoring Agent, and set SSL options on each server. This process allows you to enable SSL for all managed items in your deployment, using the provided CA file for connections by managed Monitoring and Backup Agents.