How do I apply a Square charge to existing customer invoice?

How do I apply a Square charge to existing customer invoice?

A customer has an estimate. They make an in person chip credit card payment through Square for the retaining invoice (20%) converted off the estimate. How do I now apply the square payment to the retaining invoice? There is a Square invoice already created and it won't let me remove the invoice without deleting the payments.

We want to be able to meet with customers and allow them to pay on the spot or via the portal at their convenience. So I assumed we could just associate a square payment with a customer invoice.