Disappearing Boy song meaning

In this song Armstrong expresses his feelings about his childhood. He was the youngest of 6 children in his family and that's probably where this kind of feelings comes from. Children (especially younger ones) in big families often feel invisible - parents can't give enough attention to each child and kids are often left alone. And so they feel forgotten, feel like they are disappearing - "Now you see me, now you don't". The author says that he's not sure where he belongs because his shyness and insecurity make him feel that if he vanishes, no one will notice.

The line "I see her and she's with him" might be referring to the author's step-father - a person he dislikes and whose presence makes him feel even more detached. Or it might be him seeing a girl he likes with another guy, which obviously makes him miserable. And so he leaves the place where he doesn't belong ("My whereabouts are now unknown"), he completely disappears.