If using Turbotax online, you can't make manual entries. The workaround would be to divide your W-2 into 2 W-2s, one that covers your SS wages and one that includes non-SS wages. Box 4 should be 6.2% of box 3, and box 6 should be 1.45% of box 5. Box 4 and 6 should generally be the same unless your income is more than $136,000. That's how you would split the W-2s.
For example, suppose your W-2 shows
1_$50,000. 2_$3500
3_$20,000. 4_$1,240
5_$20,000. 6_$290
You would enter this as if it was a W-2 for
1_$30,000. 2_$0
3_$0. 4_$0
5_$0. 6_$0
and another one for
1_$20,000. 2_$3500
3_$20,000. 4_$1,240
5_$20,000. 6_$290
Split the state wages and withholding in the same way.
The W-2 with zero SS tax would be marked as clergy, and you would select to pay SE tax on your wages plus housing allowance. The W-2 that shows your income that was taxed would not be coded as clergy, just as a regular W-2.
If using Turbotax installed on your own computer, you can use this workaround or you can make a manual entry as follows. Enter the W-2, check "clergy wages" and check the box for "pay SE tax on wages plus housing allowance." Then, click the Forms icon at the top to switch for Forms mode, and locate the Schedule SE Adjustment Worksheet (Sch SE Adj Wks). Locate line 5a, which is your income subject to SE tax. Highlight line 5a and select Override from the menu. Edit the line 5a amount to be only the part of your wages that were not already subject to social security tax (in my example above, that would be changing "$50,000" to "$30,000.") Be aware, however, that making overrides voids the Turbotax accuracy guarantee and prevents e-filing, you will have to print your return and file by mail.
Or you certainly could see a professional this year. Turbotax can't automatically handle a clergy W-2 that was prepared incorrectly by the church.
