ProSeries uses the same 'engine' as TurboTax, so the entry is similar in both programs.  This is how TurboTax instructs its users to do it (the latter part about Box B not being checked is just entering it on Line 21 of Schedule 1/Form 1040):

As a retired minister, you can exclude the rental value of a home (plus utilities) furnished to you by your church as a part of your pay for past services, or the part of your pension that was designated as a rental allowance, from your gross income. Any allowance in excess of this amount is considered taxable income.

If you're not already on the 1099-R screen, open your return, search for 1099-R and select the Jump to link in the search results. Follow the directions to import or manually enter your 1099-R.

How you account for the exclusion depends on whether or not Box 2b (taxable amount not determined) is checked.

If Box 2b is checked

1. Subtract your documented housing expenses from the gross distribution amount in Box 1.
2. Enter the result in Box 2a, Taxable Amount, if it's a positive number.
   • If the result is a negative number or 0, enter 0 in Box 2a.

If Box 2b is not checked

1. Enter your 1099-R exactly as you see it and complete the 1099-R section.
2. Search for other reportable income and then select the Jump to link in the search results.
3. Answer No to Did you receive other wages? and select Continue.
4. Scroll all the way to the bottom of the Let's Work on Any Miscellaneous Income screen and select Start next to Other Reportable Income.
5. Answer Yes to Any Other Taxable Income?
6. On the Other Taxable Income screen, type Clergy Housing Allowance in the description and enter your documented housing expenses as a negative number up to the amount reported in Box 2a Taxable Amount (precede the expenses with a minus sign, like -10,000).

This will remove the nontaxable portion from the distribution reported on your 1099-R.