For the purpose of allocating common expenses. If both sides of the duplex are essentially the same you can simply split it in two.  If one side is significantly larger, I suggest doing it proportional by square footage.

When posting your mortgage interest to your personal Deductions & Credits. Below the input screen for BOX 1 Mortgage Interest there is a check box for "The interest amount I entered is different than what's on the 1098".  When you select [CONTINUE].  You will have an opportunity to explain why it is different.  You can then feel confident that that it is posted correctly.