say you have 1200s lights for 3 filters, Ha, OIII, SII. the bias and darks for these 3 types of lights are the same.
the only thing that differs is the flats.
the BPP script tries to match the lights with it's respective calibration frames. so in theory you should be able to throw all of your subs into the BPP script together and it will figure it out, applying the right flats. of course it needs hints: fits keywords or filename keywords describing the filter name (and the duration) in the lights and flats.
if you have lights of varying duration, it should figure that out too, either by scaling the darks (if there is only one duration of dark loaded), or by picking from the different duration darks you've loaded to find an exact, or close match to the lights being calibrated.
rob