You have to allocate the personal portion under the Deductions & Credits. You are correct-the program doesn't not know that your rental property is part of the same home.
Think of your duplex as a separate unit, not part of your home. Enter the all the expenses that are relevant for just the rental unit. Then allocate 1/2 of interest, insurance, property taxes, (and any other shared expenses) to the rental side.
On the personal side, deduct 1/2 of interest and property taxes. Not all shared expenses (like the insurance for example) will be deductible on the personal side.