public class CustomScalableFreeformRootEditPart extends ScalableFreeformRootEditPart {

    public static final String CUSTOM_LAYER = "Custom layer";

    ...

    @Override
    protected void createLayers(LayeredPane layeredPane) {
	super.createLayers(layeredPane);
        FreeformLayer customLayer = new FreeformLayer();
        customLayer .setLayoutManager(new FreeformLayout());
	layeredPane.addLayerAfter(customLayer , CUSTOM_LAYER, LayerConstants.SCALABLE_LAYERS);
    }
}

public class ParentEditPart extends AbstractGraphicalEditPart {
    
    ...

    @Override
    protected void addChildVisual(EditPart childEditPart, int index) {
	IFigure child = ((GraphicalEditPart) childEditPart).getFigure();
        if (childEditPart instanceof CustomEditPart) {
            getLayer(CustomScalableFreeformRootEditPart.CUSTOM_LAYER).add(child, index);
        } else {
	    super.add(child, index);
        }
    }

    @Override
    protected void removeChildVisual(EditPart childEditPart) {
        IFigure child = ((GraphicalEditPart) childEditPart).getFigure();
	if (childEditPart instanceof CustomEditPart) {
            getLayer(CustomScalableFreeformRootEditPart.CUSTOM_LAYER).remove(index);
        } else {
	    super.remove(child);
        }
    }
}