Note: The Basic plan does not support multiple domains. Upgrade your plan to Pro+ to get access to multiple-domains, unlimited policies, and more.
Each cookie scan is specific to one website, so to run a cookie scan for each of your websites, you will need to run the scans individually.
You can do so on your Dashboard by clicking Scan Settings under Cookies. Then selecting Scan Now.
Switch websites using the drop-down box at the top of the page, then perform the scan again.