Hi there, KSK,

You've come to the right place, I'd love to help apply the deposit to the invoice to remove the outstanding balance.

Let's first locate the deposit, here's how:

1. Click Accounting on the left panel.
2. Locate the bank account where the payment was direct deposited into, then click View register.
3. Locate the deposit and click it.
4. Click Edit.

After that, let's link the deposit to the invoice. I'll walk you through:

1. Select the customer from the Received From column.
2. Select Accounts Receivable from the Account column.
3. Click Save and close.
4. Click the plus (+) icon.
5. Select Receive Payment.
6. Select the customer.
7. Place a check next to the invoice and deposit.
8. Click Save and close.

Now, the invoice is marked as paid. I've added this article for your future reference: Linking a Deposit to an Invoice

Thanks for giving me the opportunity to help. I'm here anytime to need further assistance with QuickBooks Online.