Yes you are correct on both points re camera connections and initial PA error.
If you have a scope with a long focal length like an SCT and are too far away from the SCP, then you may want to do an initial PA through your guide scope, then do it again through the imaging scope.
When doing the left/right up/down adjustments I don't even look at the image anymore, I set my camera for 4 second exposures and just focus on the Polar Align Error Results at the bottom of the screen.
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