On the Bill Payment screen, your e-bills needing payment will be displayed on the right hand side.  You may notice an e-bill in this area that you have already paid.  This may happen if you have made a payment to a payee but did not associate that payment to a specific incoming bill or you made the payment through other means such as by mailing them one of your personal checks or by paying them on their own website.  Therefore, the e-bill may still show as unpaid within Bill Payment.

In this case, you can simply click File for the e-bill. 

The e-bill will no longer show up as pending.  You can always view old e-bills by selecting View bill history from the menu pictured below.  If you wish to discontinue e-bills for the payee, then expand the payee details by clicking on the small arrow to the right of the payee name, and then click on Cancel e-bill.