Is this for rental income reported in box 1 of the 1099-MISC? If so, then you don't need to enter the 1099-MISC at all, so long as you include the income on the SCH E. Just tell the program that you don't have any rental income reported on a 1099-MISC, and then make sure that income is included on the SCH E, spread across the properties in the amounts that apply to each property.
Understand that when you enter a 1099-MISC, it's not sent to the IRS by you. In fact, not even the fact that the income came from the 1099-MISC is even included in your e-filed return that gets transmitted to the IRS.
