A deposit is sum of money you pay in advance for a future purchase.
To manage deposits, you have three options:
if the deposit is non refundable and you need to generate an invoice for it, you can use the Prepaid Purchases feature:
run a sale with a deposit amount (with a 'Deposit' product), add the amount paid to the Prepaid account of your customer, and deduce the deposit on the final sale. More information.
if the deposit is refundable and you don’t need to generate an invoice, you can use the Store Credit feature:
the deposit is added to your customer Store Credit account and can be used to pay the final sale (with the CRED payment method). You can print a receipt for the deposit. More information.
if you want to register the final sale at the deposit payment, you can use the Deferred payment feature. The sale is paid with an instant payment (the deposit) and a payment with a due date. The final sale (and taxes linked to this sale) are registered the day you receive the deposit. More information.