When you have rental income in box 1 and royalty income in box 2 on the same 1099-MISC, then you must enter it "AS IF" you have two physically separate 1099-MISCs.
Enter the first 1099-MISC and report the rental income in box 1 only. Then finish working through the rental in it's entirety.
When done, click the "Add another rental or royalty" and this time make sure to change the default selection from rental income, to royalty income. Then enter a 2nd 1099-MISC using the amount in box 2 only, to report the royalty income.
When done correctly, the SCH E line 3-20 will show the rental income/expenses in column A and the royalty income/expenses in column B.
