I think what you're saying here is that you entered your rental information using your own records AND received a 1099-MISC - probably from a property manager - that's reporting the same information that you've already entered. IF that's correct THEN there's no need to ALSO enter the 1099-MISC. To do so would end up in some double reporting of income.
Don't be concerned that the IRS will somehow not "see" the 1099-MISC in your income tax return because absolutely no detail about a 1099-MISC gets transmitted to the IRS in your income tax return, even though TurboTax instructs you to enter the payer's name, payer's TIN, etc. All that happens when you enter a 1099-MISC is that those dollars show up somewhere in your income tax return, and you've, (I think), already have those dollars entered.
Tom Young