In TurboTax, you will enter each side of the duplex as its own property. So on the screen you will see two Schedule E entities. It may appear that you will have two Schedule Es, but the reality is that one paper Schedule E will report up to 3 properties.
The pros for doing it this way, as two separate properties, is simply to keep everything separate. They can have different dates placed in service without trying to manually prorate depreciation and expenses. I cannot think of any cons, other than the rare occasion where you will need to prorate an expense that is truly for both properties (like your roof example).
