Continuity mistake: When SpongeBob says he should sacrifice himself, the squidosaurs Rex has Mr. Krabs in his hands, but when SpongeBob walks to the counter, Mr. Krabs is right next to Squidward. When the camera zooms in on a group of citizens and Squidward, Mr. Krabs is gone. Then, another shot of the squidosaurs Rex, Mr. Krabs is in his hands again.
Continuity mistake: When Squidward scares the people off, some of the burgers they drop disappear and change position.
Continuity mistake: During the sequence of plankton about to steal the krabby patty formula, there's a ship in a bottle on Mr. Krabs desk. When SpongeBob arrives with a vacuum, it's gone.
Continuity mistake: When SpongeBob and his crew are stranded on pelican island, Squidward releases a puddle of ink on the ground because he is nervous. When SpongeBob dabs the pen in the ink, in the next shot the ink is completely gone.
Continuity mistake: Spongebob and Plankton are stuck between a large crowd. Some are facing their backs to the Chum Bucket, the others are facing their backs to the Krusty Krab. Later, the group facing their backs to the Krusty Krab disappears.
Continuity mistake: When Patrick is holding SpongeBob, he yells to the others that he has him. Two shots later, the background of SpongeBob, Patrick and plankton has changed - specifically, the pineapple house disappears.
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