Enter the information from the 1099-R into TurboTax as it appears on the 1099-R form, including the taxable amount. You do not indicate that it's a QCD on that screen. After you enter the 1099-R, proceed through the interview in sequence. It will ask you a series of questions about the IRA distribution. You will come to a screen that says "Transfer to Charity?" That's where you indicate that it's a QCD. On that screen, if you answer that you had all or part of the distribution transferred to charity, it will be shown as a QCD on your tax return.
