If your source images are rotated by 90 degrees, then you will get better results if you rotate them before importing them to ICE.
For fine-grained adjustment of the rotation you should use the "orientation tool" (note: not available for "planar motion"). This is accessed via the "Tools>Orientation" menu item, or by pushing the cube icon in the toolbar. Once in this mode
you can perform fine adjustments of the panorama rotation. When finished just hit "Apply" to re-compose the panorama in the new orientation.