I'm not sure why you'd want to polish the sides. I guess you're taking photos or selling them? I tend to turn them round between centres and then polish them as if they were a finished pen. Those are the ones which get photographed.
I've had really bad luck with this. My blanks always look correct from the cut sides, with the top and bottom rarely being representative of the pattern. If I have crush, it sinks almost to the bottom so it can't be seen from top or bottom and in the case of swirls, the different colours sink at different rates, so I find I have to get it perfect to the millisecond or else the swirl might not even BE visible from the top!