Hmm even in the first quest it doesn't seem like Atomos is helping anyone but doing his own thing. Just like in FFXI Atomos is just kinda there doing his thing.

It helps us passively, for example in WoTG Atomos lets us travel back to the past (thanks to Cait Sith mainly) and Abyssea he lets us travel to another dimension, but he is not friend or foe unless you determine what he's doing is good or bad. More will probably be explained soon ;p