Unclear from your question.
Most clergy are common law employees and should receive a W-2 (even though they are considered "Self-employed" for certain tax purposes, they are common law employees for most other purposes.) Your taxable wages go in box 1, federal withholding in box 2 (this is allowed but uncommon). Boxes 3-6 should be blank.
A housing allowance must be designated in advance and in writing. This can be by a vote of the church council or board of deacons that is recorded in the minutes, or it could be provided to you in a letter. If properly designated, it is not reported on a W-2 or 1099. You may see some churches report the housing allowance in box 14, but box 14 is for information only and any numbers in box 14 don't impact your tax return. Or the church can simply issue a memo or letter telling you what your housing allowance was. This housing allowance IS subject to self-employment tax but not income tax.
If $14K was your entire salary from church #1 and it was properly designated in advance and in writing as a housing allowance, then the church should not have issued a 1099 or W-2.
If $16K was your entire salary from church #2 and it was properly designated in advance and in writing as a housing allowance, then the church should not have issued a 1099 or W-2 either.
Your first step would be to contact church #1 and ask them to cancel the 1099-NEC (issue a corrected 1099-NEC with zero dollars in box 1). If they refuse, then you have a couple of options when preparing your return.
If the wages were not designated in advance and in writing as a housing allowance, then they should be on W-2s and you pay income tax and self-employment tax.
Before I go into exact solutions, can you respond to my comments so far and confirm or correct my assumptions?
