I have a JFrame.
I also have a Box class which extends Component. This box class has a paint method which
Thank you for all your answers.
Since I am using my own custom class, Box, I have the ability of setting the position of my the rectangle through the paint method.
I realized my Box class was extending the wrong thing. It should have been extending javax.swing.Jcomponent.
If I now use a panel with an OverlayLayout, add my components to that panel, they all show up properly.