As long as you report as least as much rental income as is reported on Forms 1099-MISC Box 1-Rents, you should be fine. Use your own accounting records to show how you allocate the total to each property, which you can provide to the IRS if they have questions.
Enter rental income and expense from your books and records under each property address as you have in the past. You don't need to enter this information under the 1099-MISC topic in TurboTax. Under the rental income topic for Schedule E, TurboTax will provide a page for income reported on Form 1099-MISC.
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