you can actually just dump all your CR2 subexposures into BPP - all the dark subs, all the flat subs, all the bias subs, all the light subs, and it should get sorted out.
if you tick the boxes that save the masters, then you can load those instead of the dark, bias, flat subs next time, and check "use master frames" on the next and subsequent runs... until you decide you need to make new darks or flats...
rob