Which option should I pick under Clergy Self Employment Tax? I am supposed to pay income tax on my wages and only social security on my housing.

[DianeW]

As clergy, the social security tax is required to be paid on all of your income, both wages and housing allowance.  As a member of the clergy you are considered a common law employee, treated as though you were self employed.  The church is not required to, and as a rule, would not withhold and match the social security or medicare taxes on your wages.

If you W2 has information in boxes other than box 1 for wages, you can add a comment for more assistance.  

[Opus 17]

In the clergy W-2 interview, most clergy should pick "both."  You pay SE tax on both housing and wages and income tax on wages only.  The other choices apply to rare circumstances only.