The automated payment you set up when you originally filed? Unfortunately, that does not get cancelled just because you later made a choice to make a separate payment. Apparently there is a way to get the auto-debit cancelled before it occurs, but not after it has already occurred.
In situations like this, the IRS computers will eventually see the double-payment, and "should" send you a refund check in the mail in the next couple months. If you are going to move to an address different from the one on your tax return, make sure you promptly send the IRS a change of address form...Form 8822
It would seem logical that payment of the bill prior to the debit would cancel the debit however whoever said the IRS was logical ... FYI this is the same thing that happens with other bills you set up on auto debit so be careful in the future.
Sadly you did not read this entire screen in the program when you set up the payment ... now all you can do is wait for the IRS to refund the excess payment ... a painful lesson to learn.
Review the screenshot below ... note where it says "to cancel payment" you need to call ....