It is important to take into consideration that dividing the total cost of an appointment to collect a deposit will reflect on the taxes.
There is no way to collect a tax-free deposit and charge the full tax for the appointment price (e.g.: For an appointment valued at $100, with 8% taxes Total price would be $108. If you ask for a tax-free deposit of $25, the appointment price is now $75 & $81 after taxes. The tax is short $2).
This would mean that either way you charge taxes on deposit as well, resulting in an overprice for the final customer or you charge fewer taxes.
Step-by-step:
From your Dashboard go to Settings and click on Appointment statuses under Scheduling
Here you need to create a new Status (eg. "Deposit"), by clicking on + Add Status button, make sure to hit Save Changes.
One thing note: If you want the appointment to appear on your calendar, payroll, work orders, etc., you will need to set this up by clicking on the "+" icon of the status and select your preferred boxs.
The next thing you need to do is to create a new appointment with the status Deposit next to the actual appointment that you want to charge a deposit for.
In the Billing section, you fill out financial information (amount of deposit, taxes). Take note that if you charge taxes for the appointment price, you will need to charge taxes for the deposit, too.
After creating a deposit "appointment" you can charge it by invoice or credit card charge
After the appointment is done, you create another invoice for that appointment for the rest of the agreed amount of your service, the same way you invoiced your deposit.