The Poseidome (where SpongeBob duels against King Neptune to make a thousand Krabby Patties and to fight Robo-Sandy in Battle for Bikini Bottom).The Atlanteans took great advances in weapons, wealth, science, art, and things that people took for granted in Bikini Bottom today. The Atlanteans traveled countless light-years from their home planet and brought the oldest living bubble on the journey, living over a million years. The inhabitants in 'Atlantis SquarePantis' have put away all weapons in an immense vault and maintain a monarchy, seeing how the Lord Royal Highness is their kind. The royal government, led by Lord Royal Highness, could be seen as a totalitarian regime. Atlantis, as seen in 'Atlantis SquarePantis,' is the mythical Atlantis itself and has no relation to Bikini Bottom whatsoever.
The Atlantis in 'Neptune's Spatula' looks different from the city in the episode ' Atlantis SquarePantis.' They either have drastically advanced in technology in the space between the two episodes or they are two different places altogether.