Enter the total amount of property tax paid in both places (business expenses and personal deductions).
In my test case, I first entered $20,000 in property tax in the business expenses. I also entered home square footage as 3,000 and office square footage as 300, so the amount of home expenses like property tax to be allocated to the business is 10%.
When I went to personal expenses for Schedule A, the field for Property Taxes was already filled in with $20,000. If so, just leave it. If it's blank, then enter the same amount as you entered back on the business expenses page (i.e. the whole amount, like $20,000 in my example).
When I had reached a stopping point, the amount of the property tax allocated to the business was $2,000 (10% of $20,000), and the amount of property tax allocated to Schedule A was $18,000, just as you would have expected.
In other words, put the total amount paid in both places. If you set up the allocation process correctly in the business section, TurboTax will correctly divide the amount between your business and your itemized deductions.
I am a bit concerned that you said "It ends up doubling" - go back and re-enter the numbers the way I said, and then check the output (this means that you will have to manually compute what your Itemized Deductions should be and what your net Schedule C income should be, for comparison). If you are doing this online, you can see the results on the left at Tax Tools->Tools->View Tax Summary.
If you are doing this with the desktop product, I believe you can see the actual forms (Schedule A and Schedule C) by going to Forms.
