Atlantis Coins are found in your inventory under the General tab. 100 Atlantis Coins are good for one Atlantis Summon, which is available during the last complete weekend of the month.
You gain Atlantis coins each time you complete a new Season 2 stage. When you complete the stage the first time on normal, you get 3 Atlantis Coins. You can gain an additional 5 Atlantis Coins for completing the stage on hard, for a total of 8 Atlantis Coins per stage. The number of coins you have earned is displayed on the map.
Completing all of Season 2 awards 300 Atlantis Coins.
Possible sources for Atlantis coins: