If you deduct a home office for the self-employed spouse and choose to deduct actual costs, you prorate property taxes between the home office and the rest of the home (according to square footage).

You then deduct the home office portion in the home office deduction and deduct the balance in the personal section of your tax return under Deductions and Credits.

Yes, that's the correct way to do it.  The personal portion of the real estate taxes should be carried to the Schedule A for itemized deductions. 

If you go through the property taxes section in Deductions and Credits, there should be information on the screen that will tell you how much has been included automatically in the itemized deductions section of your return.  You should not enter the amount in both places (home office and property tax deduction).

@stevek