Thanks to all for your help and observations. It turns out that what got me off track was not knowing that I had to edit preferences for Format Explorer > DSLR_RAW to check the Create RAW Bayer CFA box to let me load my .CR2 images correctly. From that point it became pretty obvious at which point images should be debayered, i.e., when ready to go from Gray to RGB.
And just for the record, the bayer pattern is in fact RGGB for the Canon EOS 60Da, as Gary stated.
Dave