If you are not paid on a W2 and then you must use the self employment business section (or if you were paid on a Form 1099-MISC), you should be sure to use the appropriate business code to enter the housing allowance amount.  

For the principal business code, use 813000 (religious organization). After you enter that business code you will get a screen about clergy income. Select "I Need to Pay Self-Employment Tax on This Income." The next screen will ask you to enter the amount of your housing allowance. 

You can go directly to the area to begin to enter your income and expense for your pastoral self employment.

1. Select the Federal taxes tab (Business tab in Self Employed Online or TurboTax Home & Biz Desktop)
2. Select Wages & Income (Business Income and Expense)
3. Scroll to Business Income
4. Start or Update 
5. Use the information above to complete your return. (see image attached).

If you have an excess of housing allowance over the amount you actually spent you should enter that excess amount as income on the self employment income section.