If you make a payment without noting the invoice to which you want that payment applied, you may have an unapplied payment. Whenever this happens, you’ll see an alert next to your Amount due in the scorecard section of your Billing summary page.
To apply a payment to your balance, email your Google Apps Support team with instructions on how you’d like your payment applied and to which invoices. You can, for example, have a payment split up between more than one invoice. (Just be sure to include the invoice numbers and the amounts we should apply to each one.)
Learn more about viewing your invoices.