If you have several boxes, simply split them and place them several feet apart. The boxes where the queen isn't will become distressed and start making wide sweeps in the air trying to find her. That's a much quicker and less disruptive way of narrowing down the search to one box.
Even with one box to search through, I sometimes still have difficulty finding unmarked queens - if it's imperative that I find her (and only if), then I resort to using a Marburg Box, but you could always use two boxes with a Q/X in-between instead. Shake the bees off a frame (or two) of brood - place them in the lower box, then start shaking bees out into the top box. Most will go down into the lower box, and eventually you'll spot that elusive queen, amongst the drones - which will also be unable to pass through the Q/X.
Hope this helps