To request a deposit payment on an Invoice, select Add/Request Payment in the Payments table.
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Select Request Payment.

Choose the payment amount, whether in dollars or as a percentage. If you would like to accept the deposit via credit card using the Stripe integration, make sure the Accept Credit Cards toggle is turned on. You can also add a note to the customer!
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Press Next and compose the email you'd like to send to the customer.
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You will see the pending payment request in the payments table.

And your customer will see the request at the top of their invoice.