In some cases, you might require deposits (or advanced payments) from your customer after you have created an Estimate or a Sales order. You can create multiple deposits for the same transaction.
Creating the Deposit
You can create a Deposit directly from an Estimate or a Sales order. This option can be found in the 'Invoices' section where you can create a deposit invoice:

Once you click on Deposit, select the percentage or the amount for the deposit and click on create:

Then save the Deposit Invoice after making sure all the information is correct:

Add the payment in the 'Payments' section, just like any other invoice:

You will find your Deposit invoices in your Invoice list:

Creating the final invoice
Once you are ready to invoice your customer, the deposits will be applied automatically as line items of the invoice:

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