I’m starting my second full year with Flow Hives and have 2 healthy, but cranky hives. I successfully split the second hive from the first with a new queen last year and both filled 2 brood boxes and I was even able to get a modest amount of honey by the end of the season. I have (3) new Italian queens coming at the end of the month, and am looking for suggestions on the best way to remove the 2 existing queens, and do another split into a 3rd Flow Hive that is standing by. Current configuration of each hive is (2) brood boxes, queen excluder, and flow super (mesquite is flowing early here). I can certainly go through each box to find the current queens, but have seen suggestions here about moving brood boxes to different locations, etc. and am looking for a suggested alternative to accomplish these tasks while avoiding making cranky bees even crankier!
That is always difficult. 
Like you, I run double brood boxes in SoCal, and when the hive is cranky, that is a lot of bees. I use smoke (of course) and then put linen tea towels over the part of the hive I am not inspecting. I have an empty brood box on top of an inner cover (to maintain the lower edge bee space) next to the hive I am inspecting, and as I inspect each frame, it goes into the empty box. I cover the inspected frames with a tea towel too. The tea towel blocks the view for the guard bees, stop bees from launching from the frame tops and keeps the inside of the hive shaded. It seems to help a lot.
Of course if you have to use a lot of smoke, the queen will often run like crazy, and you won’t find her until you get to the last frame of the bottom brood box. 
I suppose that is part of the fun of beekeeping.
Hope that might help you a bit. If you don’t have tea towels, you can use canvas, old pillowcases or left over cotton fabric. Don’t use a hand towel - bees get stuck in the cotton loops and get quite upset!
The tea towels are a great idea! I’ve learned to do inspections around mid-day when the foragers are out and busy, and that helps somewhat with the hostility level. Do you inspect the top brood box first, or move it aside and start with the lower, or does it make any difference?
Thank you for the reference - I had read this before but forgotten a lot of it - especially the placement of the frames in the new box. I’ll have a new queen for the split and had planned to take an even number of various frames from each of the existing hives. I did a split from a single brood box last year with a new queen, resulting in both the split and the original hive having to “catch up” for a while - better position this year.
That is what I usually do. If I am solo, I don’t have the strength to lift a full box in any case. However, with the tea towels constraining the bees, it doesn’t seem to matter much which way you do it. Just make sure you have at least 4 tea towels (or pillows etc). That way you can keep most of the frames covered for much of the time.
Hello Michael and thank you for your contributions to the beekeeping world! Really! Question though: Recently took an advanced beekeeping course where I was told that doing splits should involve introducing a caged queen or a capped queen cell (the kind raised in queen rearing yards) or otherwise a capped swarm cell from your own yard. We were told that letting a split raise their own queen from young eggs introduced from the split is a bad idea as it only produces poor queens. In your experience, is this the case? Do you get large and robust queens from walk-away splits? Have you tried both to compare the quality of queens produced? Thanks!
Not meaning to be rude, seeing as this question was directed at Michael. I can vouch for strong robust queens from a walk away split.
In the natural world, bees frequently have to make emergency queens. This could happen after attacks from bears, honey badgers or humans. It stands to reason that they would have to make strong robust queens in order to keep the species, as a whole strong.
I have some information on the topic here:
http://www.bushfarms.com/beesemergencyqueens.htm
The fact is the circumstances, time of year, available forage, strength of the colony, availability of drones, has more to do with the quality of queens than whether it is an emergency queen. Almost every queen rearing system out that used by the queen breeders to produce your queens uses queenlessness as the trigger. So basically, other than swarm queens, they are all emergency queens. The quality or lack of it is not caused by them being an emergency queen but by doing a walk away split at a time when the resources to make a good queen are not available to that colony either because it is weak, short on bees or it’s not a good time to do it (no drones, nectar, pollen etc.).
UPDATE - MISSION ACCOMPLISHED! Was able to find both queens and was able to do my split yesterday, thanks to a combination of Dawn’s tea towel method and following Michael Bush’s instructions on dividing to conquer. I used pillow cases to cover the tops of the open boxes while I was working in the others, and that worked beautifully - I will always use that method from now on. I didn’t have enough bottom boards, but found that the lids to some plastic storage bins are large enough and are ridged to provide bee access to come and go, so I could move the boxes to a table a few yards away while inspecting. I placed an empty box on the original bottom board for the field bees as they came back, then combined all when through. The first hive is gentler, and went like a dream. The second, which was a split I made last year, is crankier and much more aggressive. Hopefully in a few months they will calm down with the new Italian queen, or they may have to go live on a farm somewhere - two sides of my property are desert, but I have neighbors and dogs to be concerned about. Anyway, I had plenty of capped brood and larvae as well as full frames of honey to do a nice split without weakening the original two hives. Have to be gone for a couple of weeks, so will see what awaits when I get back! Thanks for the help!
Thank you so much for the feedback. Makes it worth answering questions, and your experience helps others too.