Well, Amy wasn't absolutely and completely dead when she was put in, so the Pandorica kept her in stasis for 2,000 years. When little Amy touched the outside of the Pandorica, it gave the pandorica information so that it could repair big Amy.

Rory is real because the Doctor rebooted the universe, so there is a certain sense in which Rory never became a Roman... and Amy's parents were always alive, etc.