Hi Dave,
Debayering takes place after raw calibration and before registration. Up to the point of debayering, the images can be kept in one of two forms: a Raw Bayer CFA image (monochrome), or a Raw Bayer RGB image, depending on how you setup your Raw Format Preference. The second kind keeps the three color panes separate, hence it takes about 3 times the disk space. Both work, and some argue (Juan included) that there is a benefit in using this format, as it allows for independent dark scaling for each color channel (always before debayering). I personally use the CFA format, since it is faster, uses a lot less disk space, and I haven't noticed any difference to using the bayered RGB format. It's true that you get only one scale factor for the whole CFA frame when calibrating with darks, but dark current being a "blind" sensor signature (meaning that no light goes thru the bayer matrix), to me it makes more sense to use the whole frame and hence get better statistics. In fact, I input "0" in the appropriate box in IC, to force the use of the whole frame for correlation/noise calculations. If you use CFA format, make sure you select "Force CFA" in IC.
I am not sure how Batchpreprocessing works (I don't use it), but I guess it will correctly accommodate your bayer format of choice.
So, in synthesis, with dslr all three color channels are pre-processed (and post-processed, if you like) at the same time. You could split them, but there is no need. And there is no need to preconvert to fits, as that takes place automatically when PI reads CR2 files (following your raw format preference or your format hint, if you input one).
Ignacio