Atlantis is a optional act you can done before going deep into Act 4 (IT) or after Ragnarok. The npc that lead you into Atlantis act is nearby rhodes stairs that leads you into the coastal area
Ragnarok is a mandatory act if you want to proceed into next dificulty , only if you have Ragnarok expansion.
Atlantis may be hard for some buidls/classes on normal difficulty, so i would do that after i complete ACT4 or during mid act, its just a trying out and see if is dificult to handle or not.
Personally Atlantis have some bugs but still have nice things to offer as more skills per mastery, its good ideia to get on sale ( as there is on steam).
