I am following Wally Shaw's instructions for the Snelgrove Board and also the Post by Enjambres here recently.
My hive had queen cells so I am following the Part 3 for when queen cells are present.
My question is what to do after I reunite the queen into the lower box and put the frames with queen cells into the upper box to create a split. How long do I leave the upper box (split) with cells on top of the Snelgrove Board? When can I move it to it's own place in the apiary?
After you move the queen back down and the frames with brood and, hopefully, queen cells back up, you can move the box immediately off of the Snelgrove Board and onto its own bottom board for placement elsewhere in the apiary. This assumes you do not want to recombine the two boxes and want the additional colony that the top box will be making when its queen gets mated. Also note that you will have some forager loss from the top box to the bottom box due to the confusion of the move if you leave the top box in the same apiary. But that may be your goal.
But the timing on this is important as well. If, after moving the queen down and the queen cells up, you wait a few days before moving the top box off of the bottom box, you might interfere with your newly emerged queen's mating flight(s). I would guess that you could safely move the top box off anywhere from Day 8 after ORIGINAL manipulation until Day 12. After Day 12, you likely have an emerged queen in the top box. I would not want to move it much after Day 12.
If not moved prior to Day 12, I would not move it prior to Day 30, or until I saw eggs or brood in the top box. After that, you should have two fully functioning colonies and can move them where and when you like.
I always leave my top box on until the new queen goes out and gets mated and starts laying. If there is any hitch in that process, you will have less trouble simply reuniting the two parts by removing the Snelgrove board. If the new queen is hatched by about the two week anniversary of the initial manipulation, (or four or five days after you moved the old queen down), she normally needs a few days to harden, a day or so to mate and maybe just a few days more for the first eggs to be found. I usually start looking for eggs 13 or 14 days after I've moved the old queen. I am never in a big hurry, though, and there is no downside to waiting a few more days.
Leaving the boxes stacked also keeps from losing more bees than you may want as the oriented ones in the top will still have their familiar entrance point.
If, OTOH, you don't want to use the cells for an open-mated queen and wish to add a mated queen, then go ahead and separate the sections, cull the cells thoroughly, wait overnight or a few hours (whatever your usual practice is) and add the mated queen.
Once you've arrested the swarm, moved the queen down and the cells up, your time-critical tasks are done. Everything left to do is on bee-time and they will do the job exactly right.
Also don't be too over-eager to move lots of bees down if you had a particularly large population to start with and you don't have a generous amount of drawn comb in the bottom section. No point crowding them into swarming a second time.