Finally, Leland Chee has posted on the Star Wars Blog about the chronology of The Clone Wars after all the time-hopping stories in the first three seasons. It looks like the syndicated episodes will actually be airing in chronological order as opposed to their original air order, and he'll be updating as the episodes air, and covers four episodes and the movie in this post. It was clear that "Cat and Mouse" and "The Hidden Enemy" would go before the theatrical film, but I'm glad to finally get the other, harder-to-place episodes in order. The only time-jumping episode from Season Four seemed to be "Shadow Warrior," which aired after the Mon Calamari arc but took place prior to it, so I'm assuming that most of the other episodes after the main characters got their redesign halfway through Season Three should already be in order.

As to how it relates to the existing EU, he says this:
All of these episodes take place early on during the Clone Wars, mere months following the Battle of Geonosis seen in Star Wars: Episode II – Attack of the Clones. Many of the dates and events on previously existing EU Clone Wars timelines have been condensed into this period before the events of “Cat and Mouse.”
He doesn't get into it any more than that, but it's good to know that they're at least dealing with this.