Although Atalanta sometimes managed to make a surprise in the Europa League and in Serie A but still, to make a surprise in the Champions League is not easy at all. So yes, even though it currently has a new format but I'm still not sure Atalanta is able to advance further in the Champions League. but even so, at least to qualify for the last 16 or maybe the quarter-finals basically Atalanta still has a chance but of course it won't be easy.
I am very sure Atalanta will make it to the round of 16 in the Champions League. They play Arsenal, Shakhtar, Celtic, Stuggart, Young Boys and Real Madrid. The only fixtures that look impossible for them here are Arsenal and Real Madrid, other than that they have a good chance of winning the rest of the other games.
Atalanta have started the season in a slow form and that has always been a problem of theirs. They start the season slowly and begin to get better as the season goes further. Despite that, I believe they will qualify for the round of 16.
I do not know if they will make it past the round of 16 because I don't know who they will be paired against, but I know they will get to the round of 16.