I do not have a Housing Allowance or Manse/Parsonage Allowance or corresponding expenses. Every time I enter this in TurboTax, I am forced to enter a corresponding expense ($0) and then incur Income Tax on the difference.
Enter the same number for the fair market value of your parsonage and your expenses. (This is correct, not a trick. The wording of the program is aimed more toward a parsonage allowance that a parsonage.)