If you have entered 1/3 of the mortgage interest into the Schedule E interview screens, then you can enter the remaining 2/3 in the Individual Deductions & Credits 1098 menu. As long as the values are not higher than what you received on Form 1098, this won't be an issue for reporting purposes.
However, if you're worried about your manual calculations, TurboTax is able to do the math for you instead. As long as you indicate in your Schedule E/Rental Property entries that a certain % of your own home was rented and input that %, TurboTax will then split the total interest between Schedule E and Schedule A based on the relative % for rental and personal use, respectively. In this case, you would enter the full mortgage interest expense into Rental, and your 1098 data as received.
More discussion and information: Allocating Mortgage Interest Between Home and Rental.
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