For instance my main domain is cp.webquest.co.nz and I set up phpmyadmin.cp.webquest.co.nz after the installation. How do I set up SSL for the phpmyadmin subdomain?
Go to the websites list, choose the phpMyAdmin website, click advanced then security. The existing SSL will be displayed there and you will have options to request a new Let's Encrypt or upload a custom SSL.
websites
advanced
security