Breathing underwater, and living under glass
Breathing underwater = living an impossible reality, where make belief of their love is the ever-present rule.
Living under glass = Living in a world that is sealed by a thin layer of lies (the glass), that they can completely see thru, but prefer not to.
This could also be seen as the narrator coming back into the story, detailing what he thinks of the characters and their situation.
To help improve the meaning of these lyrics, visit "Thru the Eyes of Ruby" by Smashing Pumpkins Lyrics and leave a comment on the lyrics box