Unreimbursed business expenses are treated just like they are for regular employees -- they are deductible if you itemize your deductions on schedule A and they are subject to the 2% exclusion rule. They get entered on the deductions and credits interview, and you need TurboTax Deluxe or higher. Your extra housing costs over the allowance are not considered unreimbursed business expenses and you can't deduct them, if your housing expenses are higher, ask the church to increase the allowance, they can decrease your cash wage equally. Other costs like special clothing, travel, books you buy for sermon prep, etc, are unreimbursed business expenses. Tithes that you give out of your income are charitable donations, they are also itemized deductions on schedule A and are entered in the deductions and credits section. Whether you benefit from itemizing your deductions depends on the total itemized deductions compared to the standard deduction.
Separately, you can also deduct your unreimbursed business expenses from the income on your schedule SE so you can reduce your SE tax owed. (Charity donations are NOT a deduction here, only your expenses directly related to your job as clergy.) But, this doesn't go on a Schedule C. To deduct these expenses from schedule SE you need access to a special clergy worksheet that is only available through the Desktop installed copy of TurboTax (on your Mac or PC, from a download or CD copy) and can not be accessed from TurboTax online, as far as I can tell. And it's a bit tricky, you have to know what to look for. It may help to have a specialist in clergy taxes help out the first time.
