Accepting a Deposit/Pre-Payment happens in the same way as taking a payment on an Invoice only the option to specify a payment as a Deposit/Pre-Payment versus a payment.

To be able to accept Deposits/Pre-payments a Trust Account will need to be setup in the General Ledger. A trust account is where all Deposits/Pre-payments will be allocated until a time as they are assigned to a particular Invoice as payment.

From an Invoice screen click on the New Payment icon 

On the payment screen be sure there are no allocated items listed.

 
Check off the payment type. Click the Save icon. Check off the print option if a receipt of Deposit needs to be emailed to the customer.
The following prompt will appear next.

 
Click Yes. The invoices screen will show the Deposit/Pre-payment as a listed item in that screen.