Although clergy are considered self-employed for income tax purposes, most clergy are common law employees of their church and should get a W-2. Typically it should have boxes 3-6 empty. In Turbotax, check the box for "religious employment" on the page of special circumstances, and answer the questions about self-employment tax and a housing allowance or fair market value of the parsonage if one is provided. Turbotax will calculate the correct self employment tax automatically.
You will only need a schedule C if he also has side income such as cash from weddings and funerals. (Use job code 183000.) The main W-2 goes in the W-2 section.
This is an important resource http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
