On the pages that follow the entry of the details from the Form 1099-R, you must mark the box or answer the question that indicates that you had a portion of your distribution paid by your IRA custodian to charities. TurboTax will then ask how much of the distribution went directly to the charities. TurboTax will exclude this amount from the amount on Form 1040 line 4b and will include the notation "QCD" next to the line.
("QCD" = "Qualified Charitable Distribution", not "Qualified Charitable Deduction")
