The management company or the government entity issuing the 1099 should also give you some kind of accounting of where that total came from so you can split the amount appropriately. Otherwise use your own records for that breakdown. FYI ... you do NOT need to enter the 1099 in the program as one entry ... in each rental property section you can simply enter the amount of rent collected per property ... no need to enter the 1099 info in the program at all since the IRS doesn't get that from your tax return. They get a copy of the 1099 from the issuer and the IRS computer adds up all the rent on the Sch E forms in your return to match it to the 1099 total.
