Custom domain SSL for Saas

Hello there,
I have a domain at Godaddy, with nameservers to Contabo - Dedicated Server. A Saas php script is installed and has a feature to use custom names by the users with CNAME records. I want to know how to use Cloudflare SSL for Saas and how to set up/configure the whole structure so that whenever a user wants to use his custom domain, it will be a secure connection to the script.

Thanks,
Nasser

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