If you have selected the option that it's a multi-family unit, and that you live in one of the units, then yes. You will enter taxes and mortgage interest in the SCH E section only. The program (not you) will take care of the splits between SCH E for the rental portion, and SCH A for the personal use portion.
One thing you will need to check though, is the property insurance which is entered in the Rental Expenses section. You "may" have to pro-rate that yourself on the SCH E, since property insurance is not deductible for the personal use part. So with property insurance it's not split between SCH E and SCH A. It goes on SCH E only, and I don't know for a fact that the program will prorate the amount you enter on the SCH E.
