I have one parsonage allowance for a retired clergy and the 1099-R shows box 2a as -0- taxable.  I do attach an Additional Information worksheet to the return explaining.

THE TAXPAYER RECEIVED FORM 1099-R FROM xxx, EIN: xxx IN THE AMOUNT OF $xxx. THIS DISTRIBUTION IS NOT TAXABLE UNDER IRC SECTION 107 AS CLERGY HOUSING ALLOWANCE.

Looking on a Turbo Tax post they have another screen if box 2a shows taxable income to subtract it out.  For us I'm guessing you would just override box 2a and mark 2b as Taxable amount not determined.