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I dont think it would matter all that much John.. I've done it both ways, and both times yielded the same result... I suppose it depends on how skewed your guide scope is, to a point... but if you point to a star just north of east, and 20~30° up, and it drifts, you're not polar aligned.... even if the OTA is skewed.. This is because lets for arguements sake, say you were using Markab to drift align on, if your OTA is pointed at it (either guide scope or imaging scope) then if it experiences drift over time, its the same as if you had pointed at the star in the main scope.
That is assuming you're setup doesn't have significant flexture.
I may be wrong, as I'm still pretty new to it all myself, however as I said, I've alligned using both at different times, with the same result.
A better test would be to do your polar alignment with only one scope on the mount.. once done, put the 2nd scope on the mount, put an eyepiece or camera in both scopes and watch what happens... If one of your scopes drifts and the other doesnt, then you're going to have a fun time taking photos..
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