If you can compare the size of Atlantis to a place that people are familiar with, it will be the largest city in the current world, Tokyo.
With a lot of structures built and different facilities housing different branches of the former Earth's technological researches, this could be considered not just a simple Waste Disposal Site but an actual technological research facility with the size of a city.
Let's say that if we're currently near the middle of Atlantis. Hikari and those with her were at the far southwestern side. Perhaps if they ran with all they had for around three hours, they would reach us. As for the location of my other Companions, they were all scattered in every direction. There were some who already met each other and teamed up just the same.
Among one of the groups, Dannae found the blueprint for the particle cannons attached to the Automatons.