Calibration frames are a necessary nuisance. During the day, I would do your BIAS frames, and then all the DARKS for the exposure lengths that you are going to do. Then do the FLATS for each filter that you use. Then make up all the masters and save them in a calibration folder. Try to include in the title as much information as you can - temperature / exposure length / what type of master. I apologise if this is like telling a grandmother to suck eggs. You can then plug the appropriate frames into the batch preprocessor or do them manually, which I prefer. Light calibration / cosmetic correction / subframe selection / star alignment and then integration. Then you have your individual L/R/G/B masters.
I am not sure if that answers your question. As for processing and producing a final image, there are hundreds of ways. Warren Kellers book is helpful, although I had to read it quite a few times before it made any sense to me.
