As Critter-3 said, the IRS only matches your total income to the 1099-Misc that they receive. There is no line item on your tax return to place 1099-Misc income. It doesn't matter if you enter the rent received at the 1099-Misc screen or the other rent received screen. Just don't do both.
That said, the "normal" way (the "flow" in the TurboTax [TT] program) is to enter the rental income at the 1099-Misc screen and don't re-enter it when asked if your received any rent not shown on a 1099-Misc. That makes the 1099-Misc part of your TT worksheets. But, as others have pointed out TT does not send that 1099-misc worksheet to the IRS. It's only for your records.
But, you don't "have to" do it that way. Either way works. Just don't enter it twice.
