It's up to with respect as to how you want to handle your scenario.
Frankly, TurboTax is not well-suited to entering the information as a whole and then having the program "do the math". In other words, you are better off doing the math (calculations) yourself and then entering those figures into the program.
Treating the house as a single unit, however, would most likely make it difficult to determine the basis of the house at such time that you sell it and/or whether you qualify for the home sale exclusion.
