Here are the steps to follow to deduct the deposit from your final invoice when you have created a deposit invoice from the initial quote:
Go to your final invoice.
Scroll down to the bottom of the final invoice.
Click on "Subtract another invoice."
If you haven't created a deposit invoice, click on the "discount or other amount to be deducted" button, write "received deposit," and note the amount of the deposit:
Even though it's possible to deduct a deposit invoice without having previously created a deposit invoice, it's advisable to create a deposit invoice for better project tracking and to keep track of pending payment amounts.
Also, consider including the amount of the deposit invoice with taxes in parentheses, so your client can immediately see the amount they have paid.