As a GitHub organization admin, navigate to the app installation page and click "Configure" to install the PR-Agent GitHub app on an organization. The user can then select which repositories to apply the permissions to, with options for global or repository-specific configurations. After installing the app, users can customize its behavior using various configuration settings, such as default command executions and override options for different teams or best practices. Once configured, users can start using the PR-Agent in their pull-request conversations or run it automatically. The app aims to empower developers to code and merge with confidence.