When entering a W-2, you check the box for religious wages and enter your housing allowance and qualifying expenses. You have to enter the HA again even if it is in box 14 of your W-2. If you are entering the HA after entering 1099-MISC with business code 813000, there may not be a place to subtract your expenses, this is a flaw of the online program that they did not seem interested to fix.
Tell me more about your situation and I can probably come up with some workarounds.
