When line 20 of your federal Form 1040-X -- Amount you owe -- contains an amount, that is what you owe as a result of amending your return, whether you owed or received a refund on your original return.
You'll still get the refund from your original return, and you’ll need to pay the line 20 amount. The direct payment you’ve set up with your bank is all you need.
Please see Line 20—Amount You Owe on page 18 of the IRS' Instructions for Form 1040X for the payment options available.