After you enter the W2 information, look for the screen below.  It will ask you the questions to enter your housing allowance and self-employment tax.  Did the W2 have the boxes 3-4-5-6 completed for the partial year?

My main question is, I've read online that it matters that 1/2 of the year was normal W2 income and the other 1/2 of the year was clergy. A previous post said to enter two different W2s but that seemed really messy to me.

Boxes 3-6 were completed for the entire year I believe.

Yes, you are correct~that would be messy, and is not recommended. You can be clergy and receive Form W-2 and/or Form 1099-MISC.

For your husband's income, I recommend you begin by entering the Form W-2 exactly as he received it.  

• To enter this in TurboTax: How do I enter a parsonage or housing allowance reported on a W-2?

For the self-employed portion of his earnings he received, you can trust TurboTax to help you capture the details, including some or all of the following:

• Housing allowance:

  • How do I enter a parsonage or housing allowance if I got a 1099-MISC?

  • Is a parsonage or housing allowance deductible?

• Income from the church: Is my clergy income subject to the self-employment tax?
• Earnings from individuals for baptisms, weddings, and funerals: Reporting self-employed income and associated expenses.

I did this but it will not let me file. 

It says: Housing W2 box should not be checked if social security or Medicare tax has been withheld on this W2. 

Your best option at this point is to request that the church issue corrected W-2 Forms. 

You should ask the church to separate the income during his employment as an employee onto 1 W-2 Form.

The other W-2 should show his housing allowance and his income earned after he was ordained.  

You will then be able to enter both W-2s into TurboTax.

For the W-2 where he is an employee, you would NOT check the box when it asks if he was a member of the clergy.  

On the W-2 form which is for his time as an ordained minister, you would select that he was a member of the clergy.   You will then be prompted to enter your housing allowance and fair market value of your expenses.