Hi, Sunny Lowe,
Are you asking in relation to photosynths or panoramas? I only ask because when I took a look at your profile, I mainly saw panoramas.
Both ICE making a panorama or Photosynth (the original Windows application) making a photosynth are completely automatic.
In ICE you can at least specify the camera motion, which can help straighten things out a little sometimes, but if the camera moved too much while shooting a panorama, then ICE won't be able to figure things out.
If you use a different pano stitcher than ICE, then you can import the flat stitch from that into Photoshop and then upload the panorama to your Photosynth account with this plugin: http://bit.ly/pstops