Starting from version 126.96.36.199, you can apply payment policies in reservations.
In the booking system: Settings => Products => Payment Policies, you can create new payment policies. There are 2 options: you can ask for a percentage of the remaining balance or a fixed amount. You also need to select the payment method.
Then on a reservation, you can automatically apply this payment policy. Under the payments tab, you have a new button ‘Apply payment policy’. This will show all policies with a payment method. Click the one you’d like to use, and it will automatically create the payment.