If you have a 1099-MISC that has income reported in both box 1 and box 2, then you will treat it as if you received two physically separate 1099-MISC forms, with one reporting income in box 1, and the other reporting the income in box 2.
Take note that when entering the 2nd one into TurboTax, your "description" for the box 2 1099-MISC must not be the same as the description for the box 1 1099-MISC. When done, the rental income of box 1 will be reported in column A of the SCH E, and the royalty income of box 2 will be reported in column B of the same SCH E.
