Record an invoice already paid

Let's make sure that this gets sorted out, Adriana.

It seems that the deposit isn't linked to the invoice. You'll want to link the payment manually. Let me guide you through the steps:

1. Open the deposit, then change the account to Accounts Receivable.
2. Click Save & Close.
3. Open the invoice, then click Receive Payments.
4. Click Apply Credits, then go to the Credits tab.
5. Select the deposit, then click Done. 
6. Click Save & Close.

This should show you in the right direction.

For your reference, you can add and match transactions for each banking mode in QuickBooks. Please read this article for more information: Add And Match Bank Feed Transactions In QuickBooks Desktop.

Feel free to let me know about the process. I'll always be right here for you if you need further assistance.