Layering Checkboxes and Radio Buttons - The wrong type is on top

I have a form that I have two type of selections for that are layered so that we can require a selection, but also allow for multiple other selections.

To do this, I have a radio button set that has the required aspect. I then have conditional checkboxes that should be under the radio buttons so they appear after the intial selection based on conditional logic. 

The problem is, no matter how I stack the radio buttons and the checkboxes, the check boxes are ON TOP of the radio button - the exact opposite of what I want to happen. They aren't even supposed to appear until the initial radio button selection has occured according to the conditions I put on the box. 

Is there something I'm missing? The radio button was recently added. Previously it was check boxes, but they were getting skipped over and blank forms were being submitted. I really don't want to redo all the logic that's attached to the checkboxes if I can just get the radio buttons to be "On Top".