For more complex scenes, you will likely want to implement hierarchies. This means that every object in the scene is connected to a parent object until the scene's root is reached. An example of this can be a torch object, whereby the flame and the torch can be separate objects, but the flame belongs to the torch, as does the torch belong to the torch holder, as does the wall forming the parent to it, and so on.
The advantage of adding such a hierarchy is that it adds order, allowing us to address certain objects in a scene by merely following the logical tree. This helps with resource management as well.
Usually, such a hierarchy is implemented as a scene graph; where each element in a scene is connected to at least one other element, terminating at a single root element—the scene itself—as shown in this diagram: