I also run all deeps (with a medium on the bottom as a pollen box) and don't do honey. Over the next two weeks I'll be rearranging my boxes and frames towards what I consider the best winter configuration. I like to get a start on it before late summer when robbing is an issue when your stacks are open too long while doing a major rearrangement. Most of the brood in my stacks is above the lowest box right now, but I am watching for the start of a downward trend, which I would help along by moving groups of frames downward, rather than moving whole boxes upwards (as I do in the spring, for instance.) My stacks are roomy: at least four deeps, often five on my strongest hives, so I am not worried about them becoming overcrowded and honey bound like I would be in the spring. I am planning to take off frames of pollen and honey from the strong hives and donate them to three less-strong colonies which I started in late May to forestall a swarm.
But a couple of caveats: we usually have a useful - and surplus-making - late flow and only a slow down to maintenance level as far as foraging during the summer. No real summer dearth like you have in the Mid-Atlantic region. So I can expect to still be loading in surplus nectar from mid-August through the end of September. YMMV.
My pre-winter goal is: a medium on the bottom that has some stores, but mostly pollen. In most years this box stays as the lowest box, and gets little to no management by me, ever. This summer, however, I used it as a honey super because I was short of equipment due to last year's EFB problems. I may spin some of the medium frames with honey, and give them back very wet, "wets" afterward so they can stow the leftovers for winter. And then put the medium back underneath for the winter. I may really regret having moved that medium into super-duty this spring.
My lowest deep (the first box above the pollen box), is where I like to have my last brood frames of the year, with nice frames of honey (and pollen) on the outside for temp stabilization. These honey frames are usually the ones I intend to cull after the winter because they've gotten old or wonky and this is their last hurrah. And they are there to fuel the last rounds of brood and will shortly be left behind as the bees move up when the temps drop. In mid/late September if I still have six frames of brood in the ten-frame box, I'm happy.
The next deep up (the middle one three during the winter), I have mostly honey with perhaps the center two or three either brood, or well-drawn but partially-filled honey frames. This area is the central core of my winter cluster area and I prefer that these combs be high-quality, relatively new combs. Outside of them, every frame is solid honey.
The top deep is straight across honey, with some pollen in frames #3 and #7, preferably summer pollen from mixed sources, not just goldenrod pollen, And ideally on the inward facing sides of those frames, with honey on the outward face. I expect to provide supplemental pollen in the late winter, but I want them to have the good stuff early on when they are starting the first rounds of brood and it's still too cold to forage.
Every year I criticize myself for not getting my reorganization done early enough to allow them to settle in and fix whatever I've done wrong. Getting it done on time this year is my central goal for the remainder of the year, along with culling out the last of the EFB-exposed frames from and replacing them with filled donor frames from the clean hives. Some of my stacks are five deeps high, so I'll have ample resources for that, I hope.
I also routinely adjust the interior dimensions of this tall stack to match the strength of the colony using follower boards and foam panels, so I might have bees wintering on triple, 5, 6, 7, 8, or 9 frame boxes. (Only have one constant width in all the boxes, so it's a smooth column.) I think bees do better with a more vertically-oriented space vs the same number of frame arranged horizontally. I try (but usually fail) to get any stack-reductions done by early Oct.
These mid-to-late-summer plans are the ones I have the least confidence in out of the whole year. I think that's because I spent my first years working out fall, winter, spring and early summer protocols. The result was that, aside from just giving them as many boxes as they needed, I kind of left the bees to shift for themselves in the summer. And then last year when I was finally ready to play around with honey harvesting I had the EFB outbreak which messed up everything (treating with antibiotics forecloses any poss. of honey harvest.) And this year I was just skating along hoping not to have a re-occurrence, while still being extremely short of clean equipment, so I haven't felt able to make any plans. As it turned out only a single hive showed any signs of EFB, so it wasn't as bad as I feared. And my strong, healthy, ones really boomed on an unexpectedly strong late spring flow. Hopefully, by next year I'll be back on track, again.
I run all deeps, open brood nest (no queen excluder). I am in queen/nuc sales, no honey sales.
I've noticed on a few hives that the top 2-3 boxes are getting full of honey and brood. They are almost honey bound. I had the urge to put another box on top to give them room.
Yet the bottom box is almost empty. Mostly pollen. Some drawn comb they aren't even using. And some undrawn frames which I had swapped in during the summer.
Why would I add a new top box when the bottom box is barely being used? I know spring box rotation is recommended, but what about summer rotation?
Well it is being used, pollen storage , cluster space, likely an off load space, out of the brood nest, maybe water storage and /or evaporation, draft blocking for brood. It looks empty to you. So if I came to your house and seen your porch was empty, and tore it off and made it a 3rd floor bedroom...... Some times we tend to over think and try to make the hive into what we want. The bees have made it what they want. Unlikely they did it wrong. 1000 years ago who went into the hollow trees and moved the combs around so the bees could survive, Like they must have got it wrong , correct??... I tend toward uninterrupted brood nest/brood nest integrity. Now I split and manage but moving frames around just to do "something" is not on my to do list . Have a goal move the frames if you must, understand the bees know what they need at least as good as you do. take a couple unused out of the bottom to bait the top, put cull frames down there to keep it filled. there are ways to use this trait.