Both Form 1098's should show up as itemized deductions on Schedule A as long as you indicate that one is for your Primary Home and the other is for a Second Home.
After you enter Form 1098, you will get to a screen that says What kind of property is this loan for? This is where you will indicate which 1098 is for your primary home and which 1098 is for your second home.
Here is a TurboTax article with instructions on how to enter more than one Form 1098.
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