Both co-exist in the same canon (even if Lucas decanonized the first series for some reasons I still don’t understand), as I don’t remember huge continuity issues within a “total” CW narrative (the end of the Ahsoka story arc even explains Anakin deep mistrust of the Jedi Council when ROTS begins, so it’s quite important material if you want to keep the PT era in your head canon):

AOTC
CW- chapters 1 to 21
TCW- movie and tvseries in chronological order
CW- chapters 22 to 25
ROTS

The 2003-2005 series is better, more focused with needed elements to strengthen Anakin’s fall (and, as a bonus, you can assume when Luke and Leia are conceived). I consider this 2 hours show the “lost” movie of the PT (well, Prequel Tetralogy in my head canon); without it there is clearly something missing. It should have been a live movie and the PT should have been 4 or 5 movies to tell its complex story. So the “CW 2D movie” stands as a patch to fix a few narrative issues. The CGI version is too long and tends to be a “war porn” show, which is not very interesting. But there is something good in it from time to time (so far I’ve really enjoyed smudger9 movie versions of the show, especially the first two episodes).