The set has three levels...
The majority of the action took place on the ground level space with the red curtain. The Phantom's lair and the Opera stage are on this level.
The second level was used for the Opera's roof and for dynamic scenes such as "Masquerade" and "Notes". The black curtain takes the scene a step away from heightened performance.
MadJax's venue space provides a third level above the scaffolding, which was used for the mysterious Phantom's appearances.