I was asking for similar thing and the ansfer is You can't.
If you make group in Qubicle then all the matrixes are baked in to 1 mesh.
There is a workaround till developer add this feature:
Just make every part of your model on the main scene.
Name elements in such a style that you can analyse them in Unity by using special "import" script.
You can put import scripts in unity and they will act every time you update your FBX file.
By analysing the names the script can rearrange whole hierarchy by repearenting every piece of your design.
I know it is a lot more work than just make id visually in Qubicle but we need to wait till current rendering tasks will be finished by the developer.
Keep up the good work Qubicle!