When entering the 1099-R into TurboTax, TurboTax has a checkbox to mark to indicate that you need to file a substitute Form 1099-R. In the CD/download version of TurboTax it's on the Tell Us Which 1099-R You Have page. In online TurboTax its on the Do any of these situations apply to you page. Enter $0 in box 2a, leave everything else the same, mark the checkbox, then enter your explanations.
