How do I apply an unapplied payment?

Hi there, @milly1.
 
Let’s start by linking your invoice to the payment received. I’d be glad to show you the steps below.
 
Here’s how: (See screenshots below for additional reference)
 

1. Go to the + New tab and choose Receive payment.
2. Type the customer’s name on the search box for customers.
3. Tick the box for the Invoice that you want to link with the payment.
4. Click Save and close.

If you are now ready to deposit in your bank the payments you received, please follow the steps below:
 

1. Go to the + New tab and choose Bank deposit.
2. In the Account box, choose your bank account.
3. Tick the box for the payments that you wanted to be deposited in your bank.
4. Hit Save and close.

There's a resource that contains multiple articles to troubleshoot reconcile issues that I recommend: Reconcile Hub.
 
I'll always be right here if you still need my help!