You can apply a payment to a single order at a time or utilize a split payment from the account screen.
Order: Look for the payment button on the details tab to open up the payment window. You can also access this screen during the completion wizard.
Account: Make sure you are on the detail tab and look for the "new payment" button. From here, enter in the payment information and then select which orders you wish to apply that payment to by clicking the checkbox next to them.
