First, read this.
http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdfSecond, if you act under the control of the church or denomination (directly or via a board of elders, etc) then you are a common law employee. What you are saying is that they don't want to do the paperwork to employ you properly. Time for a sermon on stewardship.
The church can designate part or all of your pay as a housing allowance. The housing allowance is subject to self-employment tax but not income tax. The designation must be in advance and in writing (such as in the board minutes, a resolution, or your contract.)
The housing allowance is not reported to the IRS by the church in any format. Your wages, if they are paying you as an independent contractor, should be reported in box 7 of a 1099-MISC form, with a copy to you and a copy to the IRS.
You then report self-employment income in turbotax. Use job code 813000. This will bring up a question about self employment tax (pay on both) and a question for the amount of your housing allowance. You self-report the housing allowance.
Note that if you have work-related expenses such as mileage or supplies, you have to adjust your deduction by the percentage of income that is non-taxable housing allowance. If 40% of your income is non-taxable housing allowance, then 40% of your work expenses are not deductible (you would only list the other 60%). This is known as the Deason rule, and to properly comply you would need to print your return, attach a statement showing how you calculated the deductible part of your expenses, and file by mail.
