In Symbient Opta, you can capture a deposit received directly from the Payment.
After having created and saved an Payment with or without Items, select the Payment that you would
like to capture the deposit for by clicking on Accounting > Accounts Receivable > Receive
Payments and from the list of orders either.
Click on the Pencil icon
Check the box and select Edit
Click the Payment Reference Number link
On the Details tab of your Invoice, select the "Make Deposit" button.
Symbient Opta will automatically open the Record a Deposit from Payment screen.