You can set the system up to automatically take a deposit at the time of booking by going to:
Account Settings> Services & Costs > Deposits
Tick the tickbox provided and the deposit will automatically be deducted from the total balance.
Alternatively, you can add part payments to bookings in the Payment section. Record the payment description, the date of payment and the payment type and this amount will be deducted from the balance.
Every payment made against a booking will appear as a line item in the Payments Report.