It depends. Each college determines which application fee waivers they accept and how they prefer them to be submitted. Because of this, you should contact the admissions office at the college you are applying to and ask which fee waivers they accept and what process you should follow.
When completing your application through CFNC, there is a fee waiver option in the payment section that allows you to indicate that you are using a fee waiver when submitting your application. Be sure to follow any additional instructions provided by the college to ensure your waiver is properly applied.