Only the movies and “The Clone Wars” 2008 series are considered canon (http://www.starwars.com/news/the-legendary-star-wars-expanded-universe-turns-a-new-page). That said I've watched two seasons of “The Clone Wars” (2008) and action seems to start later than “Clone Wars” (2003) and align without any inconsistencies.
@marek-saji Not sure now in the Disney days. But back then, George Lucas said this series was the prequel to the 2008 one
Shout by Adrian RădulescuBlockedParent2014-04-14T08:57:06Z
A little (way) over the top, and I'm not sure if it is canon anymore (or if it ever was) now with the introduction of the Clone Wars animated series (that I haven't seen at this point).
It's quite good however - from an animation and cinematography point of view. Much more interesting and enjoyable than the clusterfuck prequel movies themselves and quite possibly my favorite piece of Star Wars fiction so far.