If you are insistent on using cells, then the advice would be to:
1. break up the hives, starting with the meanest, into nucs and move the nucs to a different beeyard at least 2 miles away. Make up 40% more nucs than the number of queens you need at the end of it, as there will be losses and failures that need to be accounted for.
2. Place one cell in each nuc, with a cell protector. Place the cells within the time window of 2 hours to 24 hours from when the nuc was made.
3. Leave the nucs alone, completely undisturbed, for 18 to 20 days. Then go check them. Look for a) did the cell emerge properly. b) are there fresh eggs. If there are eggs but the cell did not emerge properly then kill the queen you find because she was raised from the original mean hive brood that was put into the nuc.
4. Collect and cage the queens you are happy with. Leave the others in their nucs or bank them as backups. Recombine the now queenless nucs bees and resources into the main hives.
5. Go requeen the meanest hives with the new queens using the push-in method outlined above.
6. Sell the leftovers as nucs or as caged queens.
It will take 8 weeks after introduction of the new mated queen to the main hive to fully know if she got bopped by mean drones or gentle drones when she mated. Kill the mean ones and do it all over again.
The main point being is: cells may seem cheap but they present alot of extra work, require sacrificing some hives to get bees and resources to make nucs, takes an extended timeline, and introduce the risk of not accomplishing your goal of changing the genetics.
Unless you are already setup at raising your own queens and have a selection program in place; there is no advantage to cells and going with mated queens is the right decision path to success for the case you described.
Hope that helps!