Well, as of yEd 3.13, you can choose "None" as initial arrangement (see option "Layout" on tab "Presentation" in the Excel Import settings). This will result in all your nodes in one place and you may place them manually as you like.
Alternatively, use "Hierachical" for initial arrangement, then manually adjust the relative locations as desired, then run "Layout" -> "Hierarchical" with option "Use Drawing As Sketch" enabled.
Aside from the above, it depends very much on the algorithm chosen for initial arrangement how much you may influence the calculated position of the elements.