Here's how:
Go to the Accounts Receivables page either by:
Clicking on Orders >> on the left menu, under Account Receivable, click on Manage **or**
From the Dashboard, click on the Past Due tab
On the Invoices tab, select the invoice(s) to apply the payment to
Click on the With Selected Invoices button
Click on Prepare Apply Payments
Key in the information as needed
Click on Apply to All Invoices