Home office only for 3 months and entered 1098 on two lines. Do I check the interest amount is different when updating it in the ded/credit section?

If you are claiming actual expenses for the Home Office Deduction, you do not have to update the interest in deductions and credits.  It is automatically computed by TurboTax.

Taxpayers using the regular method (required for tax years 2012 and prior), instead of the optional method, must determine the actual expenses of their home office. These expenses may include mortgage interest, insurance, utilities, repairs, and depreciation.

Generally, when using the regular method, deductions for a home office are based on the percentage of your home devoted to business use. So, if you use a whole room or part of a room for conducting your business, you need to figure out the percentage of your home devoted to your business activities.  Use the link below for related or more information:

The Home Office Deduction