I'm trying to enter a 1099-MISC, but it isn't giving me a box 2 for entering royalties (which is what I have to report)--the first box I see to complete is box 3

That's because you're trying to enter this on the wrong form and in the wrong section of the program. You're in the Business Income & Expenses (SCH C) section, and you should be in the Rental & Royalty Income (SCH E) section.

First, you need to delete the SCH C or you won't be able to e-file. To do that, select the Personal Income tab at the top. Then choose what to work on and scroll down to the Business Items section. Elect to update Business Income & Expenses (SCH C) and you'll see your "business" listed there with a delete button next to it. Click that button, then YES to confirm the delete and work it on through to leave the business section.

Then elect to start/update Rental & Royalty Income (SCH E) and go from there.