The form 1099-R as you describe shouldn't show as taxable on your tax return. So, you can enter it so the IRS will be able to match it up with their copy. Then, prepare a substitute form 1099-R to report the taxable earnings and penalty.
You would make an entry for a substitute form 1099-R and put the withdrawal amount in box 1 and the earnings in box 2(a). You will see an option to create a substitute form 1099-R on the screen that says Tell Us Which 1099-R You Have when you go to enter the form 1099-R. Code the substitute form 1099-R as "8" in box 7, for excess contributions plus earnings and a code "J" which will result in the penalty being reported on form 5329.
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