Read this article and figured out how to add multiple layers on a single Scene.
Instead of calling replaceScene
we can just add another layer by
[[CCDirector sharedDirector] pause]; //Pauses current scene
[self addChild:[GameOverNode node]]; //adds the GameOver Layer
The added layer's buttons remain active while the GamePlay layer is paused. GameOverNode is still another class.
Hope this is helpful for any one who has a similar problem like mine.