After Mr. Krabs founded the Krusty Krab 2, he made Squidward the manager, but at the end of the movie, SpongeBob became the manager.
The Krusty Krab 2 is not seen in any other SpongeBob episode. Probably because the movie takes place after the series itself. As a reference, there was going to be a second Krusty Krab for a commercial in As Seen on TV. It will most likely appear in the upcoming second movie.
The way both restaurants were close to each other is a reference to Starbucks.
In the video game, King Neptune destroys the restaurant floor, so that is possibly why it does not appear anymore.
March 7: Grand opening of the Krusty Krab 2. Squidward becomes the manager.
March 8: The Krusty Krab 2 closes down.
March 14: The Krusty Krab 2 reopens, and SpongeBob happily becomes the new manager.
Unlike other restaurants with the exception of the Krusty Krab, it is literally and officially the second restaurant Krabs ever owned.
The reason that it was never torn down by Plankton is unknown.
It's the only time that Mr. Krabs doesn't change the name of the place instead buying it.