Yes, check the box to indicate that the amount you are entering is different than what is on your 1098. Generally, the person paying the expense gets to take the deduction. In your situation, each of you can only claim the interest that you actually paid.
As indicated by TurboTax, only enter the amounts that you are liable for. If everything is split evenly, only report half the mortgage interest, outstanding mortgage principal, mortgage insurance premiums, and property taxes.
See this IRS FAQ for more information.