One way is to use widget.SetScreenRect(x, y, width, height); -- exactly as you would with OnGUI. This function uses top-left corner as XY, just like OnGUI.
widget.SetRect(x, y, width, height) is another way -- it uses XY as bottom-left corner, which is how the coordinate origin everywhere except Windows.
You can also simply set the widget's transform.localPosition manually. It's in pixels.