Darrell,
I use AA6 all the time for spectroscopy so not a lot of experience in AP imaging.
Under the help tab, the in-built Guide/Manual has a section camera control/ sequencing which allows you to set-up your various filters for different exposures....
To process the LRGB files look at the Preprocessing guide under Help/Tools.
This allows you to set up the darks/ flats for each filter in the sequence.
Which AA forum? The old Yahoo forum is no longer supported..
This is the current forum:
http://www.astroartforum.net/forum/
Fabio is very responsive and helpful. If you still have problems with the AA forum let me know I can fix it.
Hope this helps.