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Hehe, thats right, load subs, darks and flats and click go. Some apps like DL even find the appropriate darks and flats in your (pre-setup) library automatically, and do the whole bunch of stacks in one go.
CCD stack requires you pick the dark and flat for each filter stack, and then align the LRGB stacked subs at the end, but its still a simple proceedure.
Registar also processes all in one go, and can even be scripted for a huge number of automatic operations with one click, including Mosaics.
Registax Im not sure about, but seem to remember its pretty automatic too.
Anyway, all the apps are easy to stack/combine with, thats what they are made for !. The time spent doing this is minor compared to tweaking in PS after that.
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