Sending a hero to a locked planet is a very bad idea, cause you mess the events up with it! Unfortunately it's a bug of the original game, that heroes can reach locked planets, but you should not do that. Could be, that further events will not work properly then.
Concerning Atlantis:
-Start the Warzone GC with all options set to defaults
-Focus on getting a fleet to Proclaush Taonas and capturing Chulak (Taonas will give you some trouble, since the Grace are in the way)
-Take Bra'Tac, SG-1, the ZPM, the Prometheus and General Hammond to Earth
-An "Explore Antartica" option should appear on the ground build tab, click it
-When that's done, make sure Prometheus, SG-1, ZPM, Bra'Tac and Hammond are still at Earth and select the new "Atlantis Expedition" option, also on ground build tab
-Spend 30 minutes waiting for it to finish
-When it's done, congrats, you've unlocked Midway and Atlantis! Also, when you conquer Atlantis, you automatically get Dr. Weir, who functions just like Mon Mothma in the regular game
Concerning McKay: you don't need him to steal tech in the Warzone GC, just "build" the tech level on Earth. If you can't build them, start the GC map with the preset Tech level again.