See Separation of Service in this TurboTax FAQ. Enter all of your 1099-R form as is. After each one you will be asked follow-up questions that will cover the penalty exceptions.
How does a 1099-R affect my taxes?
IRS Tax Topic 558 - You won't have to pay the 10% early withdraw penalty. Distributions made to you after you separated from service with your employer after attainment of age 55 are exempt from the penalty.
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