I have a multistory dungeon with a stair system at one side.

Unfortunately, if I attack someone on story 1, people on story two will hear it and run to the stairs, down, through a few min-use doors along the way and then join the fight.

Is there a way to prevent sounds from leaving a room? maybe by using room markers (which I have) or a magic wall I can place between the 2 floors?

Disable them on the other floor. Then put a trigger zone on the stairs, so they are enabled when the player goes up the stairs, and enters the trigger zone.

Sounds good, thanks.