You no longer need to record a payment since you've recorded a deposit already. You'll just need to link the deposit to the invoice. When matching transactions, you'll match the downloaded transaction to the deposit.
Here's how you can link the deposit to the invoice:
Open the deposit.
Change the account to Accounts Receivable (A/R), then click Save and close.
Open the invoice, then click Receive payment.
Under Credits, make sure to choose the deposit, then click Save and close.
Feel free to get back to me if you need more help with this. I'm just around.