the idea of BPP is to handle the drudgery of matching your darks with your lights, and for mono cameras, matching all your flats with your lights... as well as automatically building the calibration master frames from the calibration subs. also BPP does the alignment step as well, and performs a "trial" integration of the aligned, calibrated lights.
yes you should always use the CFA check box if you are using an OSC or DSLR. this is because the alignment step performed by BPP needs to be performed on debayered images if the input images were from OSC or DSLR.
for a mono camera you would leave CFA unchecked. CFA means "color filter array" - the bayer matrix.
rob