As long as u have the quest unlocked and zenith equipped you are doing it right. The drop rates are just very low and completely random. I spent around 50 hours farming fates (capped seals multiple times) without getting a single one. Then one day I got 3 in under an hour. It's just random. My advise is to not go for it exclusively over long hours. Spend an hour every time u log on and then go do other things. Don't worry about when other people get them, it's going to happen. A few FC mates have gotten their atma weapon in under 10 hours of farming. It's just random. Keep at it and get into full parties if you can, this makes you beat fates a lot faster.

PS: This can be a great time to level your chocobo companion from 1-10 if you haven't already. This makes it feel like at least you are making progress on something even when getting no atma.