Rob,
No, I'm doing the calibration and integration by hand. I'm asking if I treat dark flats the same as I would a bias in terms of calibrating darks with an integrated master dark flat in order to create a master dark. This is my current workflow, adapted from Light Vortex, and modified to use dark flats:
Stack bias dark flat frames to produce a master dark flat. Transform this into a noise-free master superbias.
Calibrate dark frames with master bias dark flat. Stack these dark frames to produce a master dark.
Calibrate flat frames with master bias dark flat and master dark. Stack these flat frames to produce a master flat.
Calibrate the light frames to stack with the master bias dark flat, master dark and master flat.
Is this correct? I hope this is clearer
PS: If my master dark frames are of the same exposure length of my flat or light, I don't need to optimize, right?