>From what I understand, bees are supposed to start at the bottom and work their way up, however my top box is the box the bees are working on and the bottom, even though there are bees down there, there aren't too many and no comb is being drawn out. I was wondering if this is ok and I should do nothing, or next time I work on the bees, should I swap the boxes around so they start filling out the other box.
I have NEVER put bees in multiple boxes and seen them start at the bottom and work up. They have ALWAYS started at the top and worked down. Apparently bees don't read beekeeping books. But I've also determined that they do much better in less space, so I install all of my packages in 5 frame mediums or 8 frame mediums. I never install them in one full ten frame box, let alone two.
> I was in the hive today, I got to see the queen, that was pretty cool. She's marked. Does that blue dot stay on for a good while or will it eventually wear off?
Rarely I've seen them wear off, but usually they last longer then her.
>I am from the NY (near the PA/NY boarder). So winters can tend to be long. When it comes time to extract honey, I am guessing that about 40 pounds of honey should be ample for the bees to live off of during that time. How's that sound?
Way too little. I try to get at LEAST 120 pounds of honey for a strong hive going into winter and we have similar winters to yours. More wouldn't hurt. More than 180 pounds is probably a waste. If they have less than that I'd feed them like crazy in the fall to try to get them up to that.
>Next, the boxes that are used to extract honey, I take it there's no sense to put those back on in the fall since the bees will have their surplus for the winter and there won't be much time for the bees to fill those back up.
Don't underestimate the fall flow. You could miss a lot of honey AND end up with a late swarm if you don't give them somewhere to put it. Also, they need to clean up the wet supers or you'll have wax moths running out your ears.
>Just doing some general maintenance on those boxes and storing them for the upcoming season should do the trick?
After the first hard freeze I would. You need the bees to keep the moths out AND you need a place for them to put a late flow. And I'd store them where they CAN and DO freeze to keep the moths out. Whatever you do, don't store them wet somewhere it doesn't get a hard freeze.