Yes, the first 1099-R for the Roth distribution requires you to know his earnings and enter that portion in Box 2a. Once that is accomplished you will be able to go forward with only the taxable amount showing on the tax return. And yes, a penalty will be part of his tax return for taking the money early.
If one of the 1099-R for the direct rollover has a code G in Box 7, then this would be a direct rollover that TurboTax will know based on the code. None of that would be taxable on the return.
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