yEd's Structure View is sorted alphabetically according to your node's default label text.
That said, I have to admit that I do not understand what you mean by "type out a straight forward flow". (Maybe you could upload some screen shots that illustrate your problem.) In any case, you cannot "type out" anything in yEd, you create elements using the mouse (typically by dragging templates from the palette into the editor area). Moreover, even though you can "reorder sections" manually (again using the mouse), you are usually better off using an appropriate layout algorithm from yEd's "Layout" menu.
