You must enter the Form 1099-R exactly as received. For a distribution that includes a QCD, box 2a must have the same amount as is in box 1, box 2b Taxable amount not determined is to be marked, box 7 must have code 4 or code 7 and the IRA/SEP/SIMPLE box must be marked. If the Form 1099-R provided by the payer is not reported in this way, the distribution is not from a traditional IRA from which a QCD could be made.
When entering the Form 1099-R from the traditional IRA, on the page that asks Do any of these situations apply to you, mark the checkbox to indicate that you transferred money to charity, then enter the amount of the QCD. TurboTax will exclude the QCD amount from the amount on Form 1040 line 4b and will include the "QCD" notation next to the line.