rental income

I own a single family home and rent out an apartment over the garage to my special needs son.  I also have a live in partner that pays me monthly rent.  If I deduct my mortgage interest and real estate taxes from one of the rental incomes it shows I pay zero taxes total but if I deduct the mortgage interest and real estate taxes in the space under my regular home expenses it shows I owe a total of $3000 taxes.  Where should I deduct my mortgage interest and taxes from?