Eventually you will want to read this. http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
Although clergy are considered self-employed for some income tax purposes, they are generally considered common law employees for most other purposes. As such, your expenses are deducted using form 2106, not schedule C, and you are not eligible for the small business health insurance deduction on schedule C. You are eligible for the Premium Tax Credit (depending on your income and family size) and any after tax costs for insurance would be a schedule A deduction but only if the premiums are more than 10% of your adjusted gross income.
Regarding the SE tax. Any compensation, including amounts that are "grossed up" to cover your share of SE tax, must be in box 1 of your W-2 as wages. For example, if you were to make $500 per week, the church might pay you $535, which you would use to cover half the SE tax. Typically, you would set this money aside and make an estimated payment to your IRS account. Here it sounds like they wrote 2 extra checks and kept the money back as withholding. That's ok as long as they actually submitted the money to the IRS via form 941, so that their form 941s, W-2 and W-3 all match.
You still owe the full 15% SE tax on your wages plus your housing allowance. You get credit for the amounts withheld, the same as if you had paid it into your own account. Because your SE tax and income tax are combined into one personal tax bill on form 1040, it doesn't matter that they withheld the money as income tax withholding, it all adds together in the same place.
This is an unusual treatment. It would be more typical for the church to gross up your weekly check by about 7.5% and then make you responsible for the estimated payments. Or, you can voluntarily particulate in federal income tax withholding each paycheck, via a form W-4 that goes into box 2. (If the church wants to do the paperwork of calculating the withholding and withholding state and federal tax and reporting it on form 941 etc.)
When I took over my church's accounting, we sent the SE tax via check to the pastor's personal IRS account using form 1040-ES (paying it for him directly into his account, instead of using form 941). I don't recommend this, and I stopped it. You and the church need to be clear on who is responsible for what in this situation. The church should not withhold FICA or medicare tax at all -- if they want to withhold federal income tax they can, as long as they credit the money correctly of course, and it all goes toward your final bill one way or the other.