LetsEncrypt SSL is not Issued and How to use sub-domain for VPS hostname?

Hi, I am a bit new in Cyberpanel and I am having an Issue with SSL. My domains are managed in Cloudflare. When I try to Issue a Lets Encrypt SSL. It shows that SSL has been correctly Issued but when I visit my site with https there is no Certificate! I have added A record for my VPS IP.Also, please guide me how to use a subdomain for my Hostname like server.example.com will take me to Cyberpanel Login Page?
Please Help!
Thanks in Advance.