First up I assume by "the manual states point North so I pointed South" you mean the direction you point the axis of the mount? If so, yes, point it south.
Do you have a laptop handy when you are doing this? If you do I would just use the inbuilt iPolar camera and the laptop to do the polar alignment (You could refine it later with the AA if you want to but I find the iPolar good enough for 1100mm focal length)
I don't have an AA so I cant comment on it specifically, but you do not actually need to plug in the handset at all when imaging using a PC, it can take a little longer for the GPS to sync up but that is about the only impact I have seen. I normally plug mine in anyway as the first thing I do when I power the mount on is use it to do a "Seek home"
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