JBR,
Method and timing! Mark your queens while at the nuc size, not wait until a full colony.
Or do it in the spring (careful - better to wait until laterin the year if you have no spares!) when fewer bees.
Divide brood in two, if double brood with a Q/E. She will be in the half with eggs, after three days.
Divide those frames, or at least the frames with brood, into two (or three) separate boxes - the queenless ones will soon be obvious from sound and movement.
From a huge double brood you are now down to 5, or less, frames. She is likely on a frame with brood; separate them into pairs and look on the inner faces after a couple of minutes.
Do it systematically and it is (usually) staightforward and not that hard. KISS principle in operation. Don't make life hard for yourself!
Try not to smoke them heavily or she may well scurry away and hide in a crevice. She will often be hiding just where the comb is holed and will move away from the light. You may easily spot her, from her size on the comb, when quietly parting two frames.
Hope that lot helps a bit.
Regards, RAB