Hi K, I'd really like to see you read up on preprocessing basics to get a solid understanding of what the calibration frames do. I and many still think Ron Wodaski's The New CCD Astronomy is a must. There is not one right way to proceed and PI certainly has some unique and wonderfully powerful ways of doing things. For PI-specific steps and sequence, Harry the Great's tutorials, RBA's and mine, and official PI tuts will walk you through it.
FWIW, here are my recommendations in a nutshell-
-Create the CosCorr template first
-Enable it in BatchPreProcessing
-Use Biases, Darks, and Flats appropriately w/ the BPP script
-Integrate calibrated, cosmetized, registered files in a separate step w/ ImageIntegration
Flat settings are quite different than what works as a starting point for Biases and Darks. Cruise the docs and the forum archives and you'll get a great understanding of what needs to be done.
