Will TurboTax make a payment to the IRS if I pay through www.irs.gov/payments first? I filed and set up a payment, then filed an amended return, which requires a check.

After I filed my original return and set up the payment for the taxes I owe, I received additional income information that required an amendment.  The original forms say, "Your return shows you have elected to pay your balance due of XXX by Direct Debit".  When I printed out the amendment forms, it now says, "You are paying by check."  I want to pay via the online method, but do not want to be charged twice.  If I pay via the www.irs.gov/payments website prior to the date I set up the original direct debit, will the original amount still be debited?