how do i have my RMD show up as a qualified charitable deduction. It is showing up as income, but it went directly from my IRA to my church

While entering your form 1099-R, if you have entered a birth date which makes you older than 70 1/2 in the tax year, TurboTax will ask you if any portion of your distribution was transferred to charity. You can then enter the amount transferred to charity.

The code in box 7 of form 1099-R must be 7 and the box IRA/SEP/SIMPLE must be checked.

TurboTax will then reduce the taxable amount by the amount transferred to charity.

A IRA QCD should be 0 taxable on 1040 line 4b and QCD written by it.  Unless you have other 1099R taxable amounts on 4b.  

  If you are looking at a summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 and make sure it’s right. For 1099R check 1040 line 4a/5a and 4b/5b for any taxable amount. 

To report a qualified charitable distribution on your Form 1040 tax return, you'll use the 1099-R (even though there's no indication that it was a QCD). Enter the info as a 1099-R and you'll be asked in one of the follow-up questions if it was a Qualified Charitable Distribution.

A qualified charitable distribution can satisfy all or part of your required minimum distribution (RMD) for the year.

Where do I enter my 1099-R?

What is a Qualified Charitable Distribution?