I'd be happy to show you how to select multiple invoices when applying a payment to one customer. All you have to do is checkmark the invoices you want to pay. Here's how:
In the left menu, click the Sales.
Go to the Customers tab.
Choose a customer you want to receive payment.
Click the New Transaction drop-down button and tap Payment.
Enter all the information needed.
Put a checkmark beside the invoices you want.
Choose Save and close, Save and new, or Save and send.