Maintaining your equipment is just part of the gig. The shaft is an extremely important part of that equation...keeping it clean and smooth is just a no-brainer, IMHO.
I use a damp ME and clean the shaft and ferrule well. I use a microfiber cloth to wipe off any excess moisture. I stand the shaft upright in-between the couch cushions for about 5 minutes, at which time I wipe it down with denatured alcohol, and let stand upright again for another 5 minutes. The denatured alcohol has no water in it whatsoever, and will extract any leftover moisture in the surface of the shaft wood left over from using the ME. 70% and 90% rubbing alcohol still contains water...which is why I use the denatured alcohol. I have found that by using this method of cleaning, that any small, shallow dingers will disappear during the process...which is a nice little bonus.
Once dry....I will use a piece of ultra fine sand paper and very very lightly sand once around the shaft....I wipe down towards the shaft collar with a microfiber cloth to remove and wood dust. Next I use the QWhiz...colored side first, on the shaft...wipe down again. Then use to burnishing side of the QWhiz...wipe down again...and then burnish away until you feel the shaft getting warm. Let it cool down, and burnish again. I do this until the shaft is baby's butt smooth. Then I burnish with a piece of leather to really seal up the wood. I have not used a wood sealer, as I have gotten amazing results with my method, and the shafts are burnished to the point of naturally sealing.
Been using this method for years, and have received raves about how nice the shafts of my cues have always been. All my team mates have me clean their cues' shafts as a result...LoL!
I actually enjoy the entire process...as it allows you to take time and inspect your cue's shaft(s) for any potential issues or damage you might not notice otherwise. I usually do it while watching the idiot box...and once you get it down to routine, takes little time.
Lastly, I will usually finish off by using Martin's Guitar Polish on the wood in the butt of my cue to clean and polish it....keeping it off the wrap, if there is one. Makes the cue shine and helps repel oils and fingerprints from your hands....smells good too!