If you were paid on a W-2, then after entering the W-2, check the box for "religious wages" on the page of special circumstances. You will then be asked about her housing allowance and housing expenses, and you will be asked how to pay self-employment tax. One of the choices is that you have an approved form 4361 exemption.
If you are paid on a 1099 – MISC form, then you need to use business code 813000 when you set up your schedule C. This is a code that includes charitable organizations and will trigger a question about your housing allowance, housing expenses, and payment of self-employment tax. You can again select that you have the 4361 exemption.