It depends on what the loans were used for.
Normally, you would only take one original loan out to purchase a home, so what the funds from the second mortgage were used for determines if that mortgage interest may also be claimed.
If you mean you are not able to enter two, just go back the the 1098 section and enter the second one.
You can do that by typing 1098 into the search box and clicking the "Jump to 1098" link
Or clicking Federal, then Deductions & Credits then scrolling to Your Home