A Form 1099-R provided by the payer does not have a place to indicate a QCD. The payer just reports a normal distribution on Form 1099-R. It's up to you to indicate that this is a QCD by answering TurboTax's question in step-by-step mode of the CD/download version or by marking the checkbox in the online version of TurboTax to indicate that some or all of the distribution was a QCD and the amount. TurboTax will include the QCD amount on line 4a of Form 1040 but exclude it from line 4b and will include the notation "QCD" next to line 4b.
TurboTax does not ask anything about the specifics of the QCD other than the amount. It's your responsibility to keep documentation that supports the fact that you made a charitable contribution in case the IRS questions the reporting of the QCD.
