I assume you are reporting this property in the Rental & Royalty Income (SCH E) section of the program on SCH E. Just work through the rental expenses section and when you come to where it asks for your 1098 information, enter the "first" 1098 first (the one for the old loan).
When done, you'll be on a screen with an "add another 1098" button on it. Click that button and work it through for the 2nd 1098 (the one you got for the new loan). PAY ATTENTION TO DETAILS on each and every screen. One of them will have a checkbox on it you will select to indicate that this 2nd 1098 is a refinance. You "MUST" check that box, or your taxes will be wrong and the program will NOT identify your omission as a mistake.
