My employer paid me extra twice over the year and then took that same amount out of my paycheck in those two months marked as federal tax withholding. My W-2 has no amount indicated in boxes 3-6. Federal taxes were withheld from the wages but not the housing allowance. So, my question is what should I mark on the page "Clergy Self-Employment Tax" asking if I want to pay self employment tax on 1) the housing allowance, 2) the wages, 3) both the wages and allowance, or 4) if social security and medicare taxes have been withheld?
Also, if my Clergy income is reported to me via a w-2 and yet treated as self-employment, can I deduct the difference in insurance premiums between what my employer pays and what it costs as an employment expense? If so, where do I claim this? If it were strictly self employment income then it would have been reported on a 1099 and I would have entered it that way and included those payments as self-employment expenses on a schedule C.
