With Serie A having a share of five clubs that will play in the Champions League next season, Atalanta will certainly play in the competition, because the difference of six points from Roma who are in sixth position is difficult to match, even though Atalanta will probably still be ahead in goal difference, so Atalanta has already qualified for the Champions League and Roma has lost the opportunity to play in the Champions League, so Atalanta's victory over Lecce not only opens up their opportunities but they have indeed got that place.
However, if I judge their performance against Lecce, it was not an impressive performance so I doubt they will be a competitive team in the Champions League unless they make some changes to their squad.
Yes you are right Atalanta has almost certainly made it into Champions League next season since they are six points ahead of Roma with only few games left. Beating Lecce recently made it even more likely they will get in which is great for team. However I do not think they played well in that game and if they want to do well in Champions League they need to get better players and play better overall. Just getting into competition is not enough they need to be able to compete with best teams in Europe and right now it is not clear they can do that.
Atalanta will now be counted among the strongest team in Italy this season due to their over seriousness this season which gave them a ticket to the champions league next season. They came from behind and took over the 5th position from Roma, which means that Roma will continue playing in Europa until they struggle to finish among top five.
This season is a very interesting one as we see the performance of different clubs as surprises and it made the season great.