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Same same.
With PHD2 (The only one I use so I cant comment on any other program) it works out the orientation for itself during the calibration routine so in essence it does not matter, but it is easier to picture what it is doing if you line it up so that RA/DEC line up with the two axis of the camera, and if you move the camera (Or rotate the guide scope, or the main imaging scope if you use an OAG) you need to re-calibrate.
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