How do I specify in my Certification Report that an appointment is pro bono and not paid?

The "pro-bono" setting is found within each individual appointment.

Go to Contacts > Client Name > Appointments section. Look for the appointment you want to make pro-bono and click on the "Session Notes" icon. On the Session Notes Screen for the specific appointment, scroll to the very bottom (just under the "Appointment Notes to E-mail to {Client Name}" section) and you'll find the "pro bono" option.

If the appointment is pro bono, check the box and then click "Save." Your system will take automatically the minutes of this specific appointment and add them to your certification report and the time will be listed under the "pro bono" column of your report.