Personally I have never done much to clean the surface of my sand beds.
If detritis collects in spots, definately siphion that out. Otherwise, if there is excessive cyano growth or other crap growing on the sand, then you probably have other husbandry issues to deal with. IME when I have my nutrient control fairly well dialed in, the sand and rock stays pretty clean without much if any manual cleaning.
As far as using the canister filter, I would just siphion out any crap and replace the water removed. Doing it as part of a water change would IMO work better, cost less in the long run, and be easier.
Just my $.02