In the Rental section, if you choose 'Let Us Calculate Expense Deductions for You', enter your Mortgage Interest and Property Tax here first. When you choose a % for part of home rented, TurboTax will put the correct amount for the rental and transfer the balance to your Schedule A. You'll have to enter the whole house amounts for other items, like utilities, insurance, etc. since they will all be allocated too.
Since you had both a 'part of home' and 'full home' rental situation, you could set up two different rentals for reporting this. If you indicate 'stopped renting (date)' for the part-year and 'begin date' for the whole house period, there won't be a conflict.
When you enter the Mortgage Interest in the Rental section, total your two 1098's. You won't need to make separate 1098 entries for Schedule A, since TurboTax will enter the amount for you from your rental entries. You can delete your 1098 entries in the itemized deduction section.
If you're using TurboTax Online, clear your Cache and Cookies after deleting the 1098's, before entering Mortgage Interest/Property Tax in the rental section if electing TurboTax to calculate the %.
@jummus
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