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In the next couple of weeks, I'm planning to split 100 colonies into 200 to 300 nucs, with basically nothing left of the original colony. I'll have queen cells ready to go. My question is, how can I easily know where the queen ends up without painstakingly tracking her down in each colony? I would be ok with leaving her in one of the nucs, but I don't want her where she doesn't belong causing problems with my queen cell. Any suggestions? How do the big commercial operations handle this?
 

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What is your equipment like? Colonies in two deeps?

If yes, equalize brood in both boxes, take one away to another yd and install a cell in each half. Don't look for the queen. Your time is worth more than a cell. Check them all in a week and the boxes w/ eggs have queens.

You can do that into nuc boxes too. Take a hive apart and put what you want into your nuc boxes and install a queen cell in all the parts.
 

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Good advice Mark. You could also equalize and throw excluders between double deeps a week before splitting. If you want to make 3 nucs out of each hive then better off placing cell into each nuc. Those queen right nucs might even get requeened with the cell.
 

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I would be ok with leaving her in one of the nucs, but I don't want her where she doesn't belong causing problems with my queen cell. Any suggestions?
Most would just break the colonies up into nucs, looking for the old queen as you go. If you miss a queen, as you said above, it will be okay.

But you could make the nucs in two rounds. Shake the bees from the top deep…into the bottom or on the ground in front of the hive…with a landing board for the bees to use as a ladder. Set up the combs in the top deep in a configuration for two nucs…a comb of honey at the side walls, then a pollen comb, then a frame of open brood next to the pollen, then two frames of sealed…then it's repeated across the deep. No bees. If there isn't enough brood in the top (6 frames) then rob some from the bottom box or another colony that has some extra to give.

Place the deep with brood etc above the parent with an excluder in between. Leave overnight. Next day, remove half the contents of the deep to a nuc box. Repeat with the other half. There will be no queens above the excluders so you don't even have to look.

You can repeat this process with the bottom box as you see fit.

So
 

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If you dont mind where the queen goes dont look, give a cell to all of them or come back in 2-3 days and look for cells built. If you have a preference of where the queen goes, the easiest way with 100 hives, especially if your moving them to a different location, is to set everything up the way you want it in seperate boxes. If you happen to find the queen put her in bottom box, if not shake the top boxes in front of hive, and queen excluder, then rest of the boxes. Then you can focus your attention on moving them the next morning. Alternatively, if you only own afew excluders and are not moving them far, you could arrange as the way before except this time smoke the heck out of them to drive them down to lowest box, whatever is left shake out over empty box in front hive. Then put excluder on, then splits. Wait a half hour or until they fill your splits to your liking to move. By the time you finish smoking a dozen the first one will be ready to move. Smoking the entrance helps drive them back up some too. Third option is just the old fashioned way, bring a chair and pair of reading glasses.
 

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I needed to find the queen in my colonies. and they are huge. after two days of searching frames and not finding queens I found out about placing a queen excluder in the middle of it. come back three days later and look for eggs. take off the queenless half. and split the queen right part in half again. If you still have at least two boxes. rinse and repeat.

As of now I have 5 hives that we have removed the queen from. each has been left with at least two mediums to continue to build a colony in. that leaves me with 19 boxes to split up. I am moving them to either nucs or queen castle compartments. You need to be ahead of the game to know you have empty frames. I started out a bit behind but was able to catch up fast. in a hive 5 boxes tall you can free up two to three in three days with certainty you are not moving your queen. Loosing my queens is not a option. These are the queens I am increasing from.
 
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