I’ve used both the canon software and autostitch, and I prefer autostitch.
I usually do one stitch with the default settings just to make sure it’s going to work out well, and then edit the options, most important being scale (otherwise you’ll end up with a tiny photo with no details).
Hugin is a pretty good piece of software I use to do stitching. One problem with it is that if you do “autostiching” with it, it loves to grab points in clouds and nearby ground for matching between photos. But, that is easy to fix when matching stuff in photos, so that isn’t a big problem.
Hmmm I like what I saw with autostich so far… I need to try some more pics with it and see how it does… I did a sweep around the living room and it worked well
One problem you have to look out for is that close stuff will tend to have parallax errors, unless you have a panorama head tuned to your camera. This is actually easier on a smaller sensor since the parallax error will be smaller.
Other things to keep constant are the exposure, focus, focal length, whitebalance. It is also important to prevent lens flare. (You might know this, but sometimes I forget to set all of that on my camera and have problems stitching it later, especially the white balance which Hugin has problems compensating for. exposure can easily be compensated for)
Here is one stitch I did last summer, in IR as well.