you can use BPP for all steps.
for each filter -
1) run BPP with flat dark subs, bias frames, flats and a dummy light (maybe 3 dummy lights, as the integration of the dummy master light may fail with only 1 dummy light)
2) make sure dark optimization is turned off (global options). this should cause BPP to ignore the bias frames and simply subtract the master dark it creates.
3) discard the dummy master light, save the master flat for the current filter
now, in a new instance of BPP, load your bias frames, your darks that match the lights, the lights, and the 3 master flats. you may need to use the Add Custom functionality to assign the filter name to each master flat. the master flat was calibrated in the first run of BPP and will not be calibrated in the 2nd run - BPP does not calibrate master flats. make sure to tick Use Master Flat (global options)...
this time you can optimize the darks or not depending on what you want to do.
1/10s exposures are not technically bias frames. while the dark signal might be negligible, a true bias frame has a duration of exactly 0 seconds. covington is focused on DSLRs and they do behave somewhat differently which may warrant modifications to the BPP script, but for a cooled astro camera, BPP as it stands should be fine.
rob