So basically, I should "only" consider the movies, as well as clone wars canon, right?
But the cgi clone wars doesn't even match the cartoon clone wars D: It's really messy.
it's another format, it's of course not going to match. They match in that they are telling different stories in the same universe, they aren't meant to play off each other, they are self contained and don't override each other.
You accept what you want to accept. To Lucas all that matters is his movies, he probably truly doesn't even care about much of the Clone Wars either since hes only partially involved. Folks consider it canon because Lucas is producer on it and some of the episodes are his idea, but he doesn't actually write or direct these stories so how much he actually approves of it all can be questionable even.
To the folks who work in the franchise, they try to keep it all part of a continuity.
Really you shouldn't worry about it and enjoy what you like. If your reading the novels or comics, then you got to consider it all. If you don't care about any of that, then only the movies will matter. But for those working on the Clone Wars, the video games, the books, the guides, encyclopedia, web source materials, etc... it all is part of one big continuity.