You have two choices that will work.
One would be to simply enter the income amount attributed to
each property in the income section for that property without saying it was
reported on a Form 1099-MISC. Keep your
Form 1099-MISC for your records along with documentation showing how you
divided the income among the properties.
If the IRS questions you, you have the documentation and an explanation. This is probably the simplest solution.
The other alternative is to enter the income as if you
received a separate Form 1099-MISC for each property. For this option you would change the amount
reported as rent to be the amount reported for each individual property when
you are working on that property’s income and expenses. Just be sure that the total amount you enter
for income adds up to the amount reported on the Form 1099-MISC that you
received. Again, keep documentation
showing the breakdown among the properties.