Do I need to modify the mortgage interest and property tax imported from my 1089 if I am allocating a % of those items to rental portion of my home?

Yes. It's simpler to just delete everything from the "your home" section under the deductions and credits tab. Then work through the program the way it's designed and intended to be used. That way you will deal with the rental stuff first.

In the SCH E section you have the option to let the program do the splits *for you*. If you elect that option and enter the 1098 in the rental section first, then based on your rental use percentages and number of days rented, the program will do the splits *for you*.

Then when you get to the "Your Home" section pay attention to detail. You'll see that portion of your 1098 mortgage interest that applies to SCH A is already there. So do not enter the 1098 again.