There are actually two RMD questions in TurboTax. The one that asks if a distribution reported on a particular Form 1099-R was an RMD and your answer is recorded on TurboTax's 1099-R form. This answer is only used to make sure that if you also indicate that you rolled over or converted to a Roth account any of the money distributed that you rolled over or converted only the amount in excess of your RMD. This answer is not used in any way to report on your tax return that you actually took an RMD because IRS provides no way on a tax return to report that any particular distribution is an RMD since such reporting is not required.
TurboTax asks a separate question not associated with the entry of any particular Form 1099-R about whether or not you completed your RMDs and, if you answer No, prompts you for the details needed to prepare Form 5329 Part IX.
