How do you mean? If you're using Cloudflare's CDN services, it makes sense to use the certificate issued by Cloudflare. Are you a Cloudflare CDN customer and did you want to move off of Cloudflare?
cPanel has built-in support for Let's Encrypt in its settings, although this can be disabled by the hosting provider (most often when the hosting provider sells certificates and wants to make it harder for customers to get them for free from Let's Encrypt). If you're using cPanel, there should be an option to get a certificate automatically; if you don't see it, you should probably ask your hosting provider for help.
There are lots of other ways to get Let's Encrypt certificates but, for a cPanel-managed site, none is easier, faster, or more reliable than using cPanel's own built-in support.