You should not change anything on your Form 1099-R when entering it in the federal section. You should enter the 1099-R into the federal section and allow TurboTax to transfer the amounts to the state forms. You may end up paying penalties or taxes that you are not required to. Also, when you go to file next year's returns, you won't be starting with accurate data. When electing to spread the tax over 3 years in the federal section, keep in mind, that each state handles these transactions differently. There will be an update to deal with the federal and state differences, but changing amounts you enter on the federal will almost certainly cause a reconciliation issue on future returns.
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