There's several ways to do this with TurboTax. You'll probably find it easiest and simplest to treat each unit as a physically separate entity. It's really easy if each entity has it's own separate metered utilities. The rental unit is entered as exactly that - a physically separate unit that is 100% business use.
Then for the unit you live in you enter that as a physically separate unit selecting the option for "I rent out a room in my house/primary residence".
