How are you looking? Starting at the top...smoking, looking, smoking, looking? Remove that box. More...smoking, looking, smoking, looking...
The best way would be to take the hive down placing each box on an upturned outer cover. Cover each box with a cloth or inner cover or what have you.
Now, which box is she most likely in. Probably not in the supers unless you smoked the bottom entrance. Maybe not in the bottom box...unless you smoked the top of the hive. So look through which box you think she might be in first. Don't bump and crash.
The trouble is that most beekeepers want to smoke a colony. Causes many queens to run away. You mention that you have runny bees in this colony. Makes it eveh more difficult. That's why you need to separate the boxes. Queen can't run to the bottom of the hive with all the other bees.