If you took out cash, that would limit your deduction - most common. Inputting the mortgage information for the program to try and figure out who has done what, cashed out, refinanced, etc is tricky. If you want to verify the correct amount - see page 3 of About Publication 936, Home Mortgage Interest Deduction .
Then you only need to make one entry of the correct interest and mark the balance below $750,000. The 1098 forms are not part of your Sch A. The IRS will look at your numbers and what they receive.