Generally, I wait until AFTER the last of the season's brood has hatched out to full workerbees, eliminating the need to separate any frames that are used for brood and honey - eventhough, in most hives (especially 2 supered hives) a good strength colony will have made the natural distinction and created their own honey-line that the queen just won't cross.
This is MOSTLY a second season or longer occurance though. Workers and queens in the first year are deep into comb building, storage and egg laying (pretty much) anywhere they can and old habits are hard to break.
I know C1 and C2 both have queens who enjoy laying in the upper boxes. Last inspection I switched some frames to coax them to stay down bottom, but it really didn't stick. Using queen excluders is fine for forcing the queen to stay in a particular box, but you better have a good nectar flow in order for the workers to accept and use the excluder.
So here in NJ, it is usually into early October that I harvest off my honey. I'll set a super aside on a scale, weight out 8 filled frames and hopefully get the minimum 80 pounds and add two partly filled frames to that and (at least until I am done) assume that is for the bees.
I'll spin off most of the excess, leaving 4 frames capped and set aside in my weather tight and insect proof super storage box. I'll ressemble the hives, see what late nectar may come into the hive and just give the hives the tilt test (tilting them forward to feel how full they seem) and if necessary on a warmer day in the Winter - I'll add back a couple frames toward the center of the super the bees are Wintered in.
Mind you - I'll be keeping the bees in a steel tool shed this year, away from all elements ESPECIALLY wind - so I am assuming that 80 pounds will be plenty of food. This past Winter I'm NOT SURE if that much food would have made it through, so having a place where you can open the hives up to add frames WITHOUT endangering the bees to fridged cold is handy and even neccessary during long Winters.
That about it - if your queens are happily laying in one super and you can harvest the other without the disruption of her brood being mixed in the frames that you plan, then collection or harvesting when you want is a good way to stimulate the bees to go and get more!!!