Atomos's main attack is Comet and will keep using it until one of the team members is knocked out. Once someone is KO'ed Atomos stops using Comet and starts drawing in the KO'ed character. Once the character is close enough, Atomos will use Wormhole, removing them from the battle after which Atomos will start using Comet again until another member is KO'ed. Rarely, Atomos casts Gravity, Graviga, Slow, and Slowga.
Speed is important here. Since Comet's damage does not factor in Defense, Defense is not what the party should be focusing on. The best strategy is to let Atomos kill one character, then attack it while Atomos is busy sucking them in. A White Mage should be constantly healing the party, while the other three members attack with the best attacks and spells they have. Once somebody is KO'ed, the White Mage should fully heal the other members, while they continue to attack. If the White Mage is KOed, it's best not to bother healing, and just focus on attacking.
Atomos is not immune to Sleep, so putting him to sleep and attacking him with spells can be a solution. Atomos won't stay asleep for long due to his Heavy status, but two Mystic Knights ready to use Sleep Spellblade works well. For an even cheaper strategy, one can cast Dark Spark on him once, then Level 5 Death.
Another good strategy (Particularly for a low-level party) is to have a team of four Samurai - one Samurai should have access to Black Magic while another should have access to White Magic. Quickly put Atomos to Sleep (Or let him kill a party member), then hammer the dimension-consuming demon through the use of Zeninage.