Shapes below other shapes are never visible if the top shape has a non-transparent fill color.
You can bring a shape to the top or send it to the back with the respective commands in the right-click menu of shapes.
Please make sure that the setting 'Draw selected elements on top' in File > Preferences > Display tab is disabled, otherwise, your shape ordering is changed whenever a shape is selected.
And please note that some of yEd's tools might change the ordering, too. This is because yEd has no explicit support for layers. Drawing in the front or back is more or less a side-effect of the internal ordering of the shapes. Therefore, I recommend to don't rely on that feature to much.
