Deductions & credits
Both amounts of mortgage interest reported on Form 1098 should be added together and reported on Schedule A, Line 8a. The amounts reported would be not be limited because the loans were not held for a full year. If you had MIP, Scroll down to the section 'Qualified Mortgage Insurance Premiums Smart Worksheet' on Schedule A too see the calculations there. Otherwise, the amount on Line 8a should appear on Line 8e and Line 10.
Check your Home Mortgage Interest Worksheet for calculations. You want to make sure you have a Beginning/Ending Date for the first mortgage, and a Beginning Date for second mortgage that is after ending date for first mortgage. If the dates overlap, the mortgage balances will be added together, unless one is indicated as a 'Refi'. Check the Home Mortgage Limitation Smart Worksheet section.
In my test return, I had two mortgage totaling over 750K and interest was not limited. You could delete your 1098 entries and re-enter.
