The current functionality for this does not exist to my knowledge. The only way to charge a deposit is to create an invoice with the procedure and cost and manually enter a charge for the deposit amount, adding "deposit" in the notes section.

These are extra steps for every single booked appointment, some of which have different deposit amounts, which presents a large opportunity for error. It would be great to apply the same rules and functionality that exist for online booking to these appointments. Perhaps a "special question" added to an intake form could be "pay deposit"-- State the deposit, refund policy, and payment options. Patients cannot submit the form until the deposit is processed.