Fish: Alright, all secondary characters, come with me.
SpongeBob SquarePants: If we're gonna be on the same team.
Plankton: Maybe I don't wanna be on the te-am! You think of that?
SpongeBob SquarePants: But Plankton everything's best when your part of a team.
Patrick Star: I can't think of a sweeter way to go.
SpongeBob SquarePants: We'll take one secret formula to go. Clear the area, citizens! There's gonna be some serious aft-kicking here.
Mr. Krabs: Without it, there will be a complete breakdown of social order.
Sandy Cheeks: Aw, nuts! I'm out of nuts.
SpongeBob SquarePants: There's the book! Now, it's our turn to rewrite the story.
Squidward Tentacles: You know what this needs? Some interpretive dance.
Answer: The first movie is actually set after the series finale of the show. This is because Stephen Hillenburg wanted the show to end at the Season 3 finale and for the first movie to conclude the series, but Nickelodeon disapproved, since the show was making them heaps of money. So the second movie is probably in line with the episodes after Season 3 and before the series finale. So no, it is probably not a prequel. If we look at it from a logical point of view, Plankton could have been released or escaped, and the Krusty Krab 2 could've closed. We don't know how far apart the episodes and movies are set in terms of time. The series has lots of inconsistencies anyway.
MikeH