For your son's return, it sounds like you will need to enter as if there are 2 1099s and also make a manual entry in Box 2a to address the taxable part for the one where there should be tax. Do not uncheck the taxable amount not determined box (this means it wasn't determined by the custodian.)
There is not a problem caused when an entry is made in the box 2a because the amount was not determined. (There would be a matching issue if a number was there and it was reduce or removed without explanation, though.)
If you don't have a separate 1099-R for the rolled-over portion, use the numbers from the internal 1099-R provided online and use code "H" in Box 7for an after-tax 401k to Roth IRA rollover.
For the portion subject to tax, use code "J" in Box 7 for an early Roth distribution where an exception doesn't apply.
[EDITED 03/25/24 12:25 AM PDT]
@RMartIndiana
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