The most detailed way to handle this would be to just enter the correct amount of rent with each property. If you use the same information from the 1099-MISC for the Payer and Payer ID, as long as the total sums up to what was reported on your Schedule E that is what matters.

For example, lets say your 1099-MISC says $10,000 for two properties and it should be $6,000 for one and $4,000 for the other. Pretend like you had two 1099's from the same payer (I'm guessing your property manager) and enter $6,000 for one and $4,000 for the other using the same information provided on your 1099-MISC for everything else but the amount.

In this way, you aren't forced to select "Just one" property.

Hi AlexanderS08. I have one rental property that is professionally managed and received a 1099-MISC which shows the total rents received. I am using TurboTax Premier, how/where do I enter the management fees and repair expenses?

Thank you so much  

Under "Income & Deductions" navigate to "Rents, Royalties, & Farms" and select "Rental Properties and Royalties (Sch. E)."

Then select edit next to the property (or if you have not set up a property yet you would add the property) and navigate to the "expenses" section. There should boxes for management or professional fees as well as repair expenses. Input your expenses in those boxes.