After entering the Royalty income from the Form 1099-MISC the program should ask you if this was from an investment or a business. You should select that is was an investment so the income and expenses (if any) for the Royalty income can be entered on a Schedule E.
Enter 1099-misc royalties in the Search box located in the upper right of the program screen. Click on Jump to 1099-misc royalties
See screenshot for box 2 Royalties