If you have one 1099-MISC for multiple rental units and want to apply a portion of the rent to each property, instead of entering a single 1099-MISC break it down and enter multiple Forms 1099-MISC as if you had received a separate Form 1099- MISC for each property.
If you make sure the total of your Forms 1099-MISC entered in the program equals the amount on the one that you did receive, it will match the IRS computers and there will be no problem.
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Real Estate Tax and Rental Property - TurboTax Tax Tips ...