As an employee minister, you can deduct the extra actual housing expenses amounts exceeds your housing allowance on a Form 2106. You will not enter that on the Schedule C which is for ministers who received a Form 1099-MISC or self employed. The housing allowance income is not subject to income tax but will be subject to Self Employed tax. ( whether it's a W-2 or 1099) The housing allowance expenses cannot be used to reduce any SE tax.
For example, if you have housing allowance of $10,000, related expenses $12,000. Your housing allowance is not taxable, you can deduct the $2000 on Form 2106, but your full $10,000 is till subject to SE tax.
I am attaching the following instructions how to enter your housing allowance amount so that TurboTax program will only calculate the SE tax on your housing allowance.
https://ttlc.intuit.com/replies/5412425
