Option #1: You should be able to 'link' the 1099-MISC to a specific Schedule C. Just make sure you 'link' them both to the same Schedule C.
Option #2 (the much easier option): Throw the 1099-MISCs away. There is no need for them. Just enter the actual amount of income received directly on Schedule C.
I would not disregard the 1099-Misc entry screens as suggested earlier as you want to make sure the income reported includes enough income to cover the total sum of the 1099's reported to IRS. In my state a state gross receipts tax is added to all income from services. Thus, the 1099's can total more than the book income that does not include that tax. I have to add a negative adjustment and add an explanatory note as to why the 1099's add up to more than the income being reported on Schedule C.
Also, you need to set up your Schedule C before you start entering the 1099's so the relevant business is a choice when you double click the entry box by the Schedule C line of box 7.