Filed ammended return before direct debit completed on original -- will it still go through?

I filed a return in March where I owed money and selected direct debit on April 16. Then I realized some information was missing on a form that would require me to owe a little less money. I immediately filed an amended return and Turbo Tax wanted me to mail in a check for what I owed in taxes (amount from original return - over payment) even though I had already signed up for the debit. I didn't want to double pay as I had a large bill -- my expectation was that the direct debit would still go through on April 16 and then later I would get a small amount of refund back from my over payment. Are my expectations correct, or is TurboTax going to cancel the originally scheduled debit because of the amended return I filed? If TurboTax is going to cancel the debit, should I hop on the IRS site and pay what I owed on the original return, or the smaller, correct amount from the amended return?