I followed what I am fairly certain is the correct process for entering all the relevant information for my back door ROTH contribution. I followed the steps here: https://thefinancebuff.com/how-to-report-backdoor-roth-in-turbotax.html.
I entered separate 1099-R information for myself and my spouse. When I entered my information, I got the expected "you don't qualify for an IRA deduction" message. However, when I enter my wife's information I don't get the same message, instead I get a screen asking if I want to deduct my IRA Contributions.
I'm not sure what to do with this. I pulled up form 1040 on TurboTax and box 4A has the right total amount (my contributions), but 4B has a figure in it (but I think it is supposed to be zero). Do I fix this by just selecting that I do not want to deduct my IRA contributions (which turns box 4B to zero)?
Yes, you should make sure that neither of your Traditional IRA contributions is being deducted on your return. Having them both be non-deductible is what makes the process not taxable on your return.
For another resource to follow with regard to entering the information into TurboTax, take a look at the following TurboTax help article:
How do I enter a backdoor Roth IRA conversion?