first, convert the CR2 to fits files using the BatchFormatConversion script. at some point juan put format hints in there, but i think that feature disappeared. so go into the format explorer, double-click "DSLR_RAW" and set it for raw CFA and no black-point conversion.
after converting all your CR2 to fits, load the fits files in ImageIntegration. you can follow the settings advice given here:
http://pixinsight.com/tutorials/master-frames/en.htmlyou have to get the CR2 files into FITS format before integration because II needs to seek within the files in a certain way that's not possible with CR2.
if you want to make a calibrated master dark, instead of BatchFormatConversion you can use ImageCalibration to subtract a master bias from each dark sub. but then of course you have to make the master bias using the recipe above.
rob