I have only one 1099 MISC covers 2 rental houses, I filed one house at atime. What should I do?

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Allocate the actual rental income to each property. You can enter the same 1099-misc information from the payer for each and the total income from the 1099 will equal and the payer information for each will be the same.

Enter under the summary screen for your rental property,in the incomes section.

For example: 1099 MISC Total = $40,000

Step 1.  Allocate the amount of income that is applicable to each property

Prop 1 = $15,000    Prop 2 = 25,000     

Step 2.  At the point where you are asked to enter your 1099 MISC, add a 1099 MISC for the amount of income for each property. 

 The payer for the two 1099 MISC will remain the same.  The total amount paid will equal the amount reported to the IRS

Note:A Real estate management company should issue you a 1099-MISC for your gross amount of rental income.

Management fees are an expense  on your Schedule E.