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If your guide scope was not aligned with the main scope and the guide scope was polar aligned, that means the main scope wasn't aligned at all....
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Don't think so. You are polar aligning the mount, not specific scopes on it. When that's done properly any scope on it should follow the stars perfectly, no matter where it's pointed.
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Following on from Rigel003's comments, as long as the mount is accurately polar aligned the scope can be pointed anywhere and the guide scope anywhere within about 20 deg, quite possibly more, of the scope and it will still track.
This is useful when imaging close to the CP where the movement is slow and there may not be enough change for the guider to follow, especially when the arcsec/pixel of the guide camera is significantly bigger than that of the main camera.
Andrew