Hello Brendan,
I use the Canon bundled software - seems to work very very well.
Conversion to 16 bit or 8 bit *.tif files are options together with resampling options. I use Adobe Photoshop 7 and it does not appear to "like" 16 bit tif images so I convert to 8 bit tiff. Maxdl and Astroart work with 16 bit tif files.
Tiff images are good for astro work. Canon will allow a wider gamut of colours in Adobe RGB format but I do not think this will buy much in astro processing.
Rgds,
Jerry.