CloudFlare works at the DNS level meaning you don't need to alter anything on your server. This said; for SSL you might want to install an SSL certificate so you can utilise Full SSL or Full (Strict) SSL modes: https://serverpilot.io/community/articles/generate-an-ssl-key-and-csr.html

The SSL differences are outlined here. The steps on how to set-up a domain on CloudFlare are also in our documentation.

Please do reach out if you need any further help.