The Deposit Payments add-on for your Bookly plugin allows you to set up a minimum amount that has to be paid at the time of booking. Each service and even staff member can be set up individually. And the deposit amount can be determined as a percentage of the appointment cost or as a hard amount.
The add-on will of course update your payment list as well and give special attention to whether a deposit was paid to cover a portion of the appointment cost, or whether it was paid in full.