When you enter the Form 1099-R, enter it exactly as reported on the Form 1099-R. TurboTax will ask if any of the amount reported on the Form 1099-R was transferred to charity. Answering Yes will cause TurboTax to ask you the amount of this that was QCD. TurboTax will include the entire distribution on From 1040 line 15a or Form 1040A line 11a but will exclude the entered QCD amount from the taxable amount reported on line 15b or line 11b. TurboTax will show the letters "QCD" next to this line.
Since a QCD can only be made from an IRA, make sure that you are marking the IRA/SEP/SIMPLE box on TurboTax's 1099-R form and that the birthdate that you entered indicates that you were at least age 70½ by the end of the year (the end of 2016 since you are using 2016 TurboTax), otherwise TurboTax will not ask the QCD questions.
