I am the first to admit that I am no expert on this but here are my 2 ct.
If using BPPS I would feed all the frames using same flats/darks/bias at one time. Then you can switch to next batch with new light frames and new flats/darks.... By choosing the same output directory all frames will be neatly laid out in their own folders. Ready for integration. Just remember to use same reference frame for all images that will be stacked (integrated) together. Otherwise they will not line up.
I can give you an example of a run I did last week. I had 10 red, 10 blue, 10 green and 20 lum frames. I used BPPS four times. Every time different flat and correct dark/bias. For each stack I picked the one with the best FWHM as reference for the star alignment. Output directory stayed the same for all runs. I did not use BPPS for integration.
So after four runs I had 4 folders named Blue, Green, Lum and Red. Each folder contained 10 or 20 images that were calibrated and aligned. Ready to be fed to the integration (stacking) process.
Hope this helps
regards
Mats