It’s simple. If your domain names are pointed at Cloudflare name servers then all you do is add your domain records and change the IP address to the broadcast IP of your server.
Example: lets say your broadcast IP is 123-456-789. Your domain is itslime.com. You would make an A record for itslime.com and enter 123-456-789 in the content area and save it.
You’ll do that for every domain you have. Virtualmin will take care of the rest. I’ve done it since day one.