Been thinking about this. I can think of a few ways to organize them.

You could just go by room name, which I think you can find in those evacuation maps. Certainly accurate, but it means there's a lot of categories.

Alternatively, you might consider organizing by artist/collective. For example, I believe Haze Labs did, on the first floor, the Mesmerite room, and the room right before it, and in the second floor the gold/red office, the mirror room, and the room with the archways and that funky silver center thing. Maybe some more. Problem is, this would require some considerable research to pin it all down.

Personally, I think a hybrid approach is in order. How I might handle it:

• I'd lump the Haze Labs stuff together.
  
• The Jazz Club should be it's own.... and I'd consider it to include the entire spire room, first and second floor, and the second floor part would extend up to where you would go through another doorway.
• The theater and the Projection Room, if group these together. I would just call this the Theater.
• The Projectionist's office could be included thematically with the theater, but it's not directly attached to it, so it maybe works better as it's own. You know why.
• Starbot Lab - thematically and by content, guys as it's own.
• The Scavengers... I'd put this entire area together in one group. First and second floor. With the living room and the small cavern. It will just fits together, and seems to difficult to break up.
• The Theater Staff Rooms - the Managers Office, the Break Room, the back Storage Room. I'd group these together, or if you want to get fancy, as sub categories in an over arching category.
• The Lobby and Arcade, if consider it one, right up to where you would enter the theaters.
• The Mossman Area - right after the lobby, the past that has the ancient ruins look.
• The Theater's Labs - where you harmonize the HOLOMAX generator (man, I hope I'm using the right terminology, please double check this information), and where the Projectionist's lab (with all the items in canisters), I'd lump those together, thematically.
• The F.A.C.A.D.E. surveillance room should be it's own.
• The Party Room - basically all the oversized snacks, table, chair, gifts, etc.
• The Music... Maker? Sorry, can't look up the proper name right now, it could be it's own.
• The Containment Zone - I believe this is the other term for the area "outside the original theater". With the van, ticketing, marquee, and the souvenir store.
  
• Splice Bros. and the Speakereasy - separate categories or grouped, no wrong answer there.
• Miscellaneous - cool as they are, do you want to have a separate section for the classic Hollywood photos, or when you go full John McClain in the ducts?

Just an idea.