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It is vitally important that you enter data in the program the way it is designed and intended to be used. If you do that, you will deal with the rental stuff first. In the rental section you will indicate that you rent out a portion of your primary residence and enter the information you are asked for. Then the program (not you) will take care of the split between the SCH E for the business portion and the SCH A for the personal portion of your mortgage interest.
It is just as important that you "read the small print" on each and every screen. While you'll see that the program will take care of "some" of the splits (such as the mortgage interest) there are some splits you will have to do manually yourself, such as the property insurance and "I think" the property taxes.
Basically, pay attention to detail, and you'll be fine.
No, you should not leave mortgage interest at zero on the Schedule E. It is to your advantage to claim the portion attributable to the rental on Schedule E, and the remainder on Schedule A.
You can claim the expenses on your Schedule E regardless of whether or not you itemize your personal deductions.
Your personal share of the property's mortgage interest and property taxes can be deducted on your Schedule A form. However, if you do not itemize your deductions, you will not be able to claim them.
TurboTax will compute the portion attributable to the rental if you follow the screens and indicate that you are renting out a portion of your home.
It is advisable to review a printed copy of your tax return before filing to be sure the allocations are reasonable based on the square footage of the rental area compared to the square footage of the personal area.
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