Include any amount of the allowance that you can't exclude on line 7 of Form 1040, as it is considered wages. A housing allowance - sometimes called a parsonage allowance or a rental allowance - can be excluded from gross income for income tax purposes but not for self-employment tax purposes.
Mark that your W-2 is for "religious employment" in the TurboTax followup question to your W-2 entry. (See screenshot below.) TurboTax will carry the unused housing allowance to the Form 1040 for you automatically, after you have entered your housing allowance calculation, and will also calculate the required Self-Employment Tax .