When you elect to have the program do the splits for you, you enter the total amount of interest reported on the 1098, in the SCH E section and the program (not you) does the split for you, based on your in service date.
Under the deductions and credits tab where you're asked to enter the mortgage interest, read the small print on that screen. If you elected to have the program do the split for you, then the small print will tell you how much of the total you entered on the SCH E, is already being included on the SCH A.You only enter the 1098 one time.
