If you have FICA and medicare withheld in boxes 3-6, then enter your W-2 as written. On the page of special circumstances, check the box for religious wages. You will be asked how you want to pay SE tax -- check "pay SE tax on housing only". Then enter the amount of the housing allowance and qualified expenses. This should result in you paying the FICA and medicare on your wages and the SE tax on the housing only so you aren't double-taxed on your wages.
See if you can get the church to fix it for 2018 though.
