I found a solution. Prusa slicer has an option to split up multiple bodies that come in as one stl file. Bringing them in as a single stl keeps them located relative to the CAD export orientation. After splitting they show up as a sub-assembly on the right information window. At that point you can edit the components you don’t want to print by calling them support blockers. Then switch the settings for the second run.
It’s a great way to keep components correctly located relative to each other but print separately.