As long as the total of the two distributions exceed your RMD amount, there won't be any penalty assessed.
TurboTax doesn't know your RMD requirement, so that information has to be input in the program by you. As long as you know you have satisfied the RMD with your two distributions, you can just say the amount of the distribution in Box 1 of each of the 1099-R forms is equal to the amount of the RMD for that 1099-R entry. Be sure to also check the box on the screen after you enter the RMD that states that the entire distribution applied to the RMD. This will eliminate any penalty determination on Form 5329.
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