CFNC is a North Carolina collaboration whereas Common App is a national organization. Some NC colleges and universities choose to use the Common App, but there is not a connection between the two application platforms (CFNC.org and Common App).
The most important thing to note is that when you use the Application Hub on CFNC.org, it will guide you to the preferred application for that college or university, such as Common App, Common Black App, Scoir, or an institution's own application platform. It's especially important during College Application Week to start in the CFNC Application Hub so that you'll be linked to the application platform on which the college is waiving their application fee (if applicable).