We recommend setting up the rental unit of your duplex as a separate property in TurboTax. The other unit is your primary residence and is not set up for Schedule E.
This allows you to separate the income, expenses, and cost basis using your own calculations. If you do this, you may allocate the shared expenses (like mortgage interest and property taxes) however you wish. If the units are identical, split the shared costs in half. Then report the entire rental portion on Schedule E (rental use = 100% for this unit). The portion that applies to your residence would go on Schedule A (Deductions & Credits).
Definitely do not report any expense twice.
The ultimate benefit of separating the properties is tracking the history for each unit, especially if the use changes in the future.
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