Atomos isn't that bad, as long as you have one person dead throughout the battle (going in with one dead character will help a lot). This is because he can't suck anyone in when four people are alive, and he just goes berserk. Just use stuff like Comet, Titan, 1,000 Needles, Ninja + Focus (basically any of your best damaging stuff at that point) and he should go down before he vacuums up your dead character.

Or you can use Black Spark + Level 5 Death to instant kill him, but you didn't list those as Blue Magic you had.

If you really want to grind, you can go to the basement in Bal Castle and use level 5 Death on the statues, and get crazy AP there. With enough patience, you could master Ninja, Mystic Knight, Ranger, Red Mage, and other jobs effectively making the rest of the game pretty easy. If you don't have level 5 Death you could use Gold Needles, but it's slower.

This is assuming you can even leave the tower; it's been a long time since I've played, but I think I remember being able to leave with the submarine.