I would enter that as if you had received two separate Forms 1099-MISC. If the royalties are for intellectual property you created as part of your compensated work, they are going to find their way back to your Schedule C, anyway. But if you do not break-out the reporting of the two income streams, I fear the IRS will have trouble matching the reported amounts from the Form 1099-MISC to your tax return, resulting in a notice requiring you to provide an in-depth explanation.
