What I did was click "add new room" in the 2D editor. It does appear that in the gamedata panel the intended separate room is in the same stack as the other stuff, though. Not sure how to fix that without breaking something.
huh i see. it doesn't work the same way for me, when i create new rooms in 2d panel they are placed in a separate stack..
well i guess you could create another stack with a couple of placeholer rooms with a few blocks, and then inspect game data and replace the room ids with the rooms ids you want to be separate from your other stack. bitsy 3d game data is in json format and punctuation is important, make sure you have all the quotes and commas in the same way like you see in the original game data, like not having a comma after the last item in a list and stuff