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Hi Peter,
Yes, you're correct. You can use either a master dark or a light frame that exhibits the bad pixels/columns you wish to reject. The master dark will have the bias included so you would think that would be a bad thing i.e as you point out, you would be be subtracting defects twice. Technically though a bad pixel map isn't subtracting anything, it just flags the pixel/column defects as a 'missing value' i.e. highlights them in red indicating they are ready for interpolation. CCDstack has info on building the map using the data rejection process. I would build the map with a master dark first to see how that works for you.
In your case, it would go something like this.
1 Calibration (bias and flat)
2 Reject bad pixel map (interpolate rejected pixels)
3 Image registration (method of choice, large stacks go with nearest neighbour, small bi-cubic)
4 Normalisation (manually select background and highlights)
5 Data rejection of choice. (STD large stacks, Poisson small stacks)
6 Mean combine (or sum as if need be for working with faint narrowband signal)
Any further outliers in your data left over from steps 1 and 2 will get rejected in step 5 - assuming you are dithering. I don't know many that don't dither between subs these days.
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