There are two different ways to use CloudFlare: basic mode and advanced mode.
Basic mode does not require you to change your nameserver or manage your own DNS records, and is set up by our cPanel Install Plugin. This is the simplest and easiest way to get going with CloudFlare.
Advanced mode will require you to change your nameservers. Once they are changed any changes you make in cPanel will have to be made to the zone file with CloudFlare by you manually. Advanced mode is only recommended for advanced users who cannot make the redirections that basic mode demands.
Note: if you attempt to add a domain via advanced mode, you will not be able to add the domain via basic mode until you remove it from the CloudFlare dashboard.
See more info about CloudFlare: