You need to do two entries for your rental property.
To further clarify, you will have two entrires in the SCH E section. One for your rental property, and a completely separate one for the royalty income.
Take a look at lines 3-22 on a blank SCH E at https://www.irs.gov/pub/irs-pdf/f1040se.pdf
When you are done, Column A would be the rental income/expenses only for the rental property. The amount of rent received would be on line 3 Column A. The amount of rent received will be in box 1 of a 1099-MISC if you received a 1099-MISC.
Column B would be for the royalty income/depletion. The amount of royalty income would be on line 4 under Column B. The amount of royalty income received will be in box 2 of a 1099-MISC if you received a 1099-MISC.
So if you received one 1099-MISC with an amount in box 1 and box 2, you would enter it "as if" you received two physically separate 1099-MISC forms. One with the rent in box 1, and the other with the royalty payment in box 2.
