Where can I indicate which clients are pro bono and which are paying?

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 > CLIENT NAME > APPOINTMENTS > “+Add Notes” button. At the top 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 select; simply schedule their appointments.