I have a number of concerns about your situation.
First of all, you can’t “arrange“ to be paid on a W-2 if you are an independent contractor. The nature of the tax document you receive depends on the nature of your employment arrangement and not the other way around. Most ministers are common-law employees of their church and should receive a W-2 even though they are considered self-employed for limited tax purposes. If a minister answers to the denomination or to the church in any way, such as by means of a board of elders, or an administrative council, or some other method whereby the church body determines the hiring and firing, or validates their “call” to ministry at that church, or however you want to describe it, then the minister is a common law employee.
Ministers would only be independent contractors at their regular church if they are truly independent of the congregation, the denomination, or any other body. “Supply pastors”, that is, temporary fill-ins for summer vacations or leaves of absences or sabbaticals, may be more commonly and more properly considered independent contractors.
Second, a housing allowance must be designated by the church in advance and in writing. I have always wondered if a truly independent pastor can ever legally have a housing allowance, since to be really independent, the pastor can’t answer to the church and therefore, there is no one in authority to designate a housing allowance. However, I have never seen this litigated or discussed in the resources I have read. So for the time being, I assume that a pastor can have a housing allowance even if they are an independent contractor.
Third, recording the housing allowance in box 14 of a W-2 has no force of law and does nothing to legitimize the housing allowance. The housing allowance must be designated by the church in advance and in writing, such as in the minutes of the board of elders or your employment contract. Box 14 is merely a memo field and has no force of law. It is just as legal to receive your housing allowance information in a memo from the treasurer or finance committee, and if the housing allowance is not designated in advance and in writing then no amount of other documentation will make it proper.
Fourth, all deductions for work-related expenses for W-2 employees are disallowed under the tax reform of 2018. If your job as a pastor is covered by a W-2, then you simply can’t deduct a home office regardless of the dollar value of the deduction. If you are using a home office partly for a W-2 job and partly for other independent contractor work (assuming that you are doing other pastoral work on the side) then you have to allocate your expenses between the W-2 job and the independent job and reduce your claimed home office amount anyway. You can’t claim home office expenses for a W-2 job on schedule C even if you also have other schedule C employment—you have to properly allocate the expenses between the two jobs. While you can enter work-related expenses In TurboTax as a W-2 employee, they will have no effect on your federal tax return. They might flow to your state tax return depending on your state and if you itemize deductions in that state.
Fifth, if you have work-related expenses as a pastor, even as a W-2 employee, you can deduct them from your income subject to self-employment tax on schedule SE, even though you are no longer allowed to deduct them on schedule A using form 2106. This requires making manual adjustments to the schedule SE worksheet, which requires you to have TurboTax desktop version installed on your own computer from a CD or download. You can’t make manual adjustments using the online program. (According to IRS instructions, it also requires that you prepare a written statement of your expenses and attach it to your tax return which means you can’t e-file.)
Finally sixth, you mention ministerial taxes at the end of your question but you never specifically said you were a pastor. Remember that you are only entitled to a housing allowance if you are both a qualified pastor in your denomination and you are performing pastoral duties in your present position. A qualified pastor who is hired, for example, to provide administrative help in the office and does not participate in leading worship or performing other pastoral tasks is not qualified for a housing allowance. Or, at my former church, we hired a pastor from another denomination as our youth pastor. He was not qualified to offer sacraments in our church until he took two required seminary courses, and so was not entitled to a housing allowance until those courses were completed.
Since you talk about the idiosyncrasies of ministerial taxes, I hope that you are not taking advantage of the church’s ignorance in tax matters to arrange your employment arrangements for tax purposes. I have found nothing concrete that says you can’t have a housing allowance as an independent contractor, despite my doubts. But whether you are an independent contractor or an employee depends entirely on the relationship between yourself and the church and has nothing to do with how you would prefer your income to be taxed. If the church is currently paying you as a employee with the expectation of issuing a W-2 at the end of the year, then they need to be sending form 941 quarterly, or form 944 at the end of the year, along with quarterly state reports—even if they are not doing any withholding they must file the forms to report that you are an employee. Backing out of this in mid year is going to be very difficult for them even if it is legitimate to do so. I would consider it a matter of proper stewardship and ethics to be classified correctly (as either an employee or a contractor) and then work within the tax laws after that, rather than trying to arrange your employment status to fit some interpretation of the tax code.
