Pub 517 is for Self-Employment "SECA" taxes and/or "FICA" (which is Social Security and Medicare) taxes as an Employee. This publication is because a cleric might be both. You have to know what they do, what part(s) fall under Employment (such as, being hired by a church) and what they do as an Independent worker (such as, in the summer they travel to RV parks in their RV, hold Tent sessions and accept money for their services at weddings, etc).

And some religious beliefs have the right to file and declare they are Exempt from Social Security, which means when they get old, they cannot collect from that system, either. For instance, they know they will get old and die in an abbey somewhere.

And anything related to the employment is not a business expense, the same as you or I would have for tax reporting.

Worksheet 1 is Source of Income. That includes the Value of things provided. For instance, Housing has a value; you don't get it for free. That value is treated "the same as money" in the computations for things that apply.

You fill in what applies in the appropriate columns, for tax treatment. That gets you to line 6. For example: some people are Only an employee of a church and everything they do is under that Church as their congregation/employer. Some people do not work for a church, or are their own church. Or, are not even associated with a church, but a military or volunteer clergy. And there are special cases. It's very complicated and there are Church Guidance tax articles on the web, which are easier to use than what you found.

Specific costs of Life in general are not necessarily tax deductions (like Electricity cost for your home). But some things are used to compare to any paid amount or allowance you are given. Example: It costs you $5,000 to rent and pay all the bills that house you and your family, but your church gives you $10,000; that difference is like Free Money, so that is taxable. Or, you are allowed to pay $300 rent for a Water-Front mansion, or No Rent for it. All of that matters.

"It compute line6 in worksheet1 then use this number to compute line7 in worksheet2."

It moves to the Top of the next worksheet, because everything will now need that piece of info for the next part for allocation.

We call this "The Accounting Principle." It means that the Expenses are related to the Income. You only report Business Expenses that relate to the income from that same Business. That's why you see that fine print: "None of the other deductions claimed in this return are allocable to tax-free income."

See how they relate the cost to the income that is specific for that cost incurred? And that means certain things are not a deduction, just like your costs for your pet's vet bills are not a tax deduction.

That's why Mileage is there. Business mileage on the Church's vehicle where you are an employee is not your business deduction. Mileage on your own vehicle that is hauling the kids to school is not your Business mileage. Using the church's vehicle for personal would be taxable to you through payroll. Using your own vehicle for your own business is part of Schedule C costs to generate that income. But not all of the miles.

Line 7 is taking into consideration things like vehicle use and meals, where you have to pro rate them if you cannot point to something and say, "That is Purely personal, Purely my employment through my church, or Purely business activity for me working not under my church as their employee."

Remember, you are working on whether that value will then be subject to SECA. That's why the worksheets get you to a Net reportable amount.

"I saw the computation like this from other software, but I cannot see this computation from Proseries."

And I do not know how to open these worksheet from Proseries."

It has different inputs and screens.

You can work through the separate forms (W-2, 1040 Sched C, 1040 Sched SE, 1099-Misc, 1099-NEC) for minister or clergy designations. And you can use google to search for topics that might help:

proseries minister

proseries clergy