The problem is not with polar alignment it's with gotos. It doesn't matter whether you polar align through the guide scope or main scope. However after alignment the asiair will expect you to do a goto and then will automatically adjust it's sky model to make the selected object appear in the centre of the field of view. If the guide scope and main scope are not aligned and the polar alignment and goto were done on the guide scope then a goto on the main scope may be way off, especially if the main scope has a large focal length like a schmidt cassegrain.
It would be very useful if asiar included a 3 star alignment routine so that after polar aligning through the guide scope you could align through the main scope.
