You do need to enter both 1099-R forms, and it is correct that your form 1040 will show both distributions.
Since the rollover funds were put into different retirement vehicles, I suggest you break up the form 1099-R entry into three separate entries, the total of which will equal the distribution amount reported on the 1099-R form. That way, you can treat each one separately and answer the questions as it applies to where each distribution ended up.
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