When you designate all salary as housing allowance, how will W2 look like as there is no wages and taxes (assuming that there is no withholding) - all boxes to zero?
If no W2 is required due to no taxable income reported, will there be no 941 required as well? (if the pastor is only employee)
If you want to DIY your payroll, I highly recommend you look at using Gusto! It is very user friendly and their support is awesome! Plus they know how to set up and maintain payrolls for churches and nonprofit organizations.
Note: I am a "partner" of Gusto, but as I have told you before ... I never recommend anything that we or our clients have not tried and love =)