This answer misses the point. The original posted noted that there is no efficient way to manage the z-order of an object when there are lots of objects in the file. With 50 objects on the page, you may have to click 153 times (click object, right-click for context menu, select "Raise selection", right-click for context menu, select "Raise selection", etc.) to set the z-order of an object to the top.
yEd ideally needs a layer manager like that in Adobe Illustrator. Or at least the crippled "Raise to top" / "Raise one layer" choices like in Microsoft PowerPoint.