When you enter your W-2, check the box for "religious wages" in the listing of special circumstances. the program will ask for the amount of your housing allowance and the amount of your qualifying expenses (which can be less or the same as the housing allowance but not more).
What do you mean, you paid for 2024 but not 2023? You should now be preparing your 2023 tax return (due April 15, 2024 for income received in 2023). Last year, you filed a 2022 tax return that was due April 18, 2023, but was for the 2022 tax year.
If you filed your 2022 return without reporting your housing allowance, you will need to file an amended 2022 return to report the housing allowance and pay self-employment tax. The HA is subject to self-employment tax even if it is not subject to income tax.