Formating Pop-up Fields in Application Builder

I know that you can modify the display format of Pop-Up fields directly in the PopUp_x.xml, such as precision or if a field should use a thousands separator etc.

But is there a way to do the same in the "Custom" section of the Pop-Up configuration in Application Builder 3.3? If I make a change in the .xml, then make a change in the "Custom" section, the previous changes made directly to the .xml go away.

Do I have to wait until after I have the "Custom" section exactly the way I want it before I edit the .xml, or can I add formating in the App Builder?

Thanks,

Jared