You have the flexibility to do this on a per-appointment basis, and you can do it either from the Calendar when you schedule/edit the appointment or in CONTACTS TAB > CLIENT NAME > APPOINTMENTS > "Take Notes" button. At the bottom of this page you can choose the "Pro-bono" option. When you click on the box next to this option and click "Save" this appointment and the time associated with it will be tracked as "Pro-bono" on the Certification Report.
By default all appointments with active clients and inactive clients (that occur in the past) are automatically recorded as paying unless you choose "pro-bono." So, for your paying clients, there is nothing to choose; simply schedule their appointments.