This is very easy, first make sure your website is working with your server. Point the A records to your server for your domain, then you can go to your website in Ploi and select "SSL" on the left hand side.
Now press the big "LetsEncrypt" button, you will be prompted for which domains you want to request, usually this is pre-filled so you can just click "Save" to get the certificate from LetsEncrypt.
If this process fails, we will detect this and send you a e-mail about it containing the error. 95% of the cases that a certificate is failed to be requested is due to the fact that the DNS record is not been setup correctly to your server.
Ploi also sets up your server for automatic renewals, you will find this specific cronjob in the /etc/crontab file.
Cloudflare users: You are not able to request an SSL certificate if you have the proxy on (orange cloud should be gray). You can disable this and then wait 15 minutes, after that request a new SSL certificate. Once that completes you can re-enable the proxy.
Please note: If you have IPv6 setup for your domain, you will not be able to request a certificate. Please remove any AAAA records before you request a new certificate.