Chris,
I’m sure after a few “dry runs” you’ll quickly get the hang of selecting the data for preprocessing.
I use AA7 for all my acquisitions- darks, flats, dark flats and target exposures.
For me the added functionality that Fabio added for stacking Spectra is majic!
Also note, that AA7 includes very capable guiding, focus control and even very quick plate solving.
For AP processing there are many tools which allow you to tweak to your hearts content.
If you have any specific issue, just drop me a PM. I’d be glad to assist.
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