If memory serves, I don't think Omega Weapon makes an appearance until Final Fantasy VIII. Atma Weapon #1 was probably the toughest boss for the time period you are in with the game. Atma #2 was really easy. If you notice real closely, the first one you fight is called Atma Weapon, the second one you fight is called just plain "Atma" - think that was on purpose?

(completely forgot about this thread)

That's it, it's in the Dragon's Den. You have to first defeat all the Eight Legendary Dragons (gaining you the Crusader Esper) and then defeat Kefka at the end of the game. In FFVI:A, instead of the game simply ending, the game actually continues and the Dragon's Den opens up. It's located on one of the small islands near the tip of the 'nose' of the land mass that looks a bit like a dragons head in the Northwest part of the world map.

I there, you split your party into 3 groups (just like Phoenix Cave and Kefka's Tower) and work your way around a vast cave, fighting new powerded up versions of the Dragons. At the end you'll face the Ninth and previously unfightable Kaiser Dragon (it was in VI if you used a code because it was actually left out the original though its data remained in the game). Defeating him allowes you to progress to Omega Weapon and your prize for defeating it is the Diablos Magicite.