If the Form W-2 and the Form 1099-MISC both reported the same payments, then you will have to make an adjusting entry to prevent double-counting the income.
First, enter the W-2 in the Wages and Salaries interview of Federal Taxes > Wages and Income (or Personal Income). Enter it exactly as it was sent to you to ensure you get credit for the taxes withheld.
Then, enter the Form 1099-MISC in the Income from 1099-MISC interview in Wages and Income > Other Common Income.
Do NOT say the income was related to your work or career, that it involved an intent to make money or that it had been received in the past or expected in the future. Answering "Yes" to any of these questions will trigger self-employment taxes.
Finally, go to the Other Reportable Income interview, the very last interview in Wages and Income (Federal Taxes > Wages & Income > Less Common Income > Miscellaneous Income ). (Or enter "other reportable income" in the Search Box and select "jump to other reportable income"). These payments are NOT wages).
Enter the amount reported on the 1099-MISC as a negative number. This will cancel out the earlier 1099-MISC entry.
