I haven't watched every Stargate: Atlantis episode, but I've watched quite a few from the later seasons and have been watching some lately from an earlier season. One thing that really confuses me is in the three part episode "The Siege" from an earlier season, the Wraith some how know about Atlantis and are attacking it. Then they pretend to blow up Atlantis and all the Wraith leave...
Later in the series the Atlantis team has help from a lone Wraith, who Shepherd met while imprisoned. This Wraith eventually learns of where Atlantis is. In those seasons it sounds like Atlantis is a secret to the Wraith, which is why they are never under attack. But clearly in the early episodes I mentioned the Wraith knew all about Atlantis and just decided to leave. Shouldn't they know about Atlantis later on too? Why don't they go back and attack? And also why did they just leave without checking the sea around Atlantis? Wasn't the whole point of not doing a self-destruct was their fear that the Wraith would stick around and check the rubble?