How do I apply unapplied payments? I have payments that were made, but I am still showing an open balance. They are sitting in Unapplied. How do I apply them?

Good day, @hareintheforest.

Let me share information on how to apply the unapplied payments in QuickBooks Desktop. 

The unapplied payments happen if invoices have been deleted, customer's overpaid, or they aren't applied to an invoice. 

In your case, you may have received invoice payments directly without applying for the unapplied payment. To resolve this, you can delete the payment link to the invoice and apply for the payment.

To delete the payment, here's how:

1. Open the affected invoice.
2. In the Create Invoices window, go to the Transaction tab.
3. Under RELATED TRANSACTIONS, it will show the deposit you use as the payment.
4. Tap the deposit transaction.
5. In the Make Deposits window, hit Edit at the top menu.
6. Select Delete Deposit.
7. Click OK to confirm the action.

Once done, to apply for the unapplied payment, follow the below steps:

1. Go to the Customers menu.
2. Choose Receive Payments.
3. Select your desired customer. You'll see the amount of the credit included in the Existing Credits field and the refund check at the bottom section of the window.
4. Choose the Apply Existing hyperlink (refer to the screenshot below).
5. Enter the amount in the Payment column, if not already entered by QuickBooks.
6. Hit OK.

For future help, I'm attaching an article below that will give you the answers you need for QuickBooks Desktop: Get QuickBooks Desktop user guides.

That's it. If you have any follow up questions or clarifications this process, please leave a comment below. Have a great day.