It is vitally important that you enter data in the program the way it is designed and intended to be used. If you do that, you will deal with the rental stuff first. In the rental section you will indicate that you rent out a portion of your primary residence and enter the information you are asked for. Then the program (not you) will take care of the split between the SCH E for the business portion and the SCH A for the personal portion of your mortgage interest.
It is just as important that you "read the small print" on each and every screen. While you'll see that the program will take care of "some" of the splits (such as the mortgage interest) there are some splits you will have to do manually yourself, such as the property insurance and "I think" the property taxes.
Basically, pay attention to detail, and you'll be fine.
