For the ONLINE version: 

When doing the returns, finish the interviews for both husband and wife. 

Then click on Income, then click on Employment Expenses Profile. The list will come up. Just put a checkmark in the box of the clergy, and obviously leave the spouse's empty. The pages will now appear for the clergy ONLY. 

Should be almost the same process on the download version. 

Exactly, for the online version, you need to click the Income tab > Employment Status Profile.

There you can select clergy residence deduction for you and then on the next page, you can input what information applies to you.

When you click continue, you will be provided with the same form as yourself regarding clergy fees but this time for your wife.

At this point, you need to leave the information sheet blank, or, she will also have the deduction.

I hope this information was helpful!