After you finished playing with re-positioning the parented cubes, press CTRL+Z to undo until it's back to being a straight stack for the next step.
"Parent" Is the parent of Child 1, Child 2, Child 3.
"Child 1" is the parent of Child 2 and Child 3
"Child 2" is the parent of Child 3
"Child 3" is only a child with no children attached.
So if you move Parent, you move all 3 childs.
If you move Child 1, you move child 2 and 3 too.
If you move child 2, you also move child 3.
After you played with rotating the parented Cubes. Press CTRL+Z to undo all of it for the next step.
Every "Copy" (Prefab) of the parent cube has the same color and the same Child1,2 and 3.
Remember to give it a name! You don't want your own custom objects to just be called "Game Object"!
Then select all your objects and click and drag into your empty game object.
HINT: Click the beginning object, HOLD SHIFT and then click the ending object to select all objects between.