You can't "claim" a housing allowance. A housing allowance must be designated by your church in advance and in writing. You and your spouse may each receive a designated housing allowance but if the total is more than your qualified housing expenses it will be added back to your taxable income.
Since that is on the honor system, you are responsible for being honest and responsible to prove your housing expenses if you get audited.
For each W-2 or 1099-MISC, turbotax has a place to indicate religious wages, the amount of housing allowance, and the amount of qualified expenses. So it's up to you when you fill out the tax return.
If you are living in a church-provided parsonage, it will be a little more complicated.
This is an excellent resource. http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
