If you have a patient pay a deposit for services, you can allocate the payment and balance their account in one of the following ways:
add a line item to the first invoice issued after the deposit was paid that reads ‘Less deposit’ with a negative amount equal to the deposit. That would decrease the total amount.
or add a 'payment' using a new Payment Method called Deposit and make this 'payment' a negative amount, to cancel out the deposit originally recorded.