I have different subfolders per project for it’s components.
Project/KiCAD
Project/FreeCAD/Model1
Project/FreeCAD/Model2
Etc.
Each project has it’s own set so it’s easy to find. I think it’s better than having all 3D printing related things together and then having to sort which project it belongs to.
Time to make the mother of all omelettes. Can’t fret over every egg!