If you are reporting two home offices, or two business uses of the same home office, you are going to have to either allocate the mortgage interest and real estate taxes between the two, or decide which home office will be the one to take those deductions. I would recommend against making an allocation, as it shifts the burden of computation onto you, rather than allowing TurboTax to do the work for you the way it was designed.
If your are attributing other common expenses (gas, electricity, water/sewer, internet, trash collection) to the home office, these too can only be taken once. If you list them on both forms, you will grossly overstate your deductions.
Finally, with reference to your Schedule A Itemized Deductions: If you are entering your mortgage interest and real estate taxes on the home office worksheet, do not enter the Form 1098 normally when going through the itemized deductions portion of TurboTax. The portion of interest and taxes not allocated to the home office should automatically carry over to your itemized deductions. Entering it again will double-count the deductions.
