Allocating overpayment to a customer

Hello cwill 

Welcome to the Community Forum.

As the situation you describe is your customer has paid a second time, what you would do is create a customer return for this second payment, which you can choose whether you want to apply the overpaid amount to an invoice or refund the customer. You can also hold onto the credit to apply to a future invoice.

I have attached a Help Article on customer overpayments for how to set this up.

Please let me know if you need further assistance.