The series happened. The Movie happened, and it was supposed to be the end of the series. SpongeBob's arc ended. He became the manager of the Krusty Krab, and he was okay with being a kid, but he still gained maturity. The series didn't need to go on after that point- It was the end. But Nick brought it back. Steve has stated that the movie is the end point of the series, and it makes sense. If it wasn't, then wouldn't SpongeBob be the Manager of the KK from Season 4 on? Wouldn't there be two Krusty Krabs? And while the show doesn't really have much continuity, it makes more sense to put the movie after everything in the series because it's a logical end to SpongeBob's character arc and the series as a whole.
Think of the movie as a Series Finale made way too early, and the rest of the show just continues off of Season 3.