Sounds like you're using very out dated OpenGL code. You should look into modern techniques, I wouldn't waste much more time learning/using the dated code you're using now.
Beyond that, there are lots of ways to organize your world and the objects you store in it. The very basic example is to just have a class that represents an object in your world:
public class DrawableObject {
Vector3f position;
Vector3f rotation;
Model model;
BoundingBox bounds;
}
Then create your objects using these classes. When you're updating the position of the orbiting objects, update the DrawableObject instance that represents them. Then when you're drawing the objects, use the position and rotation stored in the DrawableObject instance.
Basically, you don't want to send the updates to the graphics card and not have them stored anywhere on the CPU side. You want to update something locally and then use that data to update the data on the graphics card.
Eventually you could move on to something more complex like an entity component system. But for now, I'd stick with learning modern OpenGL and keeping track of the objects in your world in a more organized way.