Deep box question
I'm a new bee keeper this year. I'm also a cabinet maker by trade, so I decided it'd be no problem building my boxes and covers. I placed a late order for a nut, and procrastinated on making my boxes. Well low and behold they called and told me my nuc was ready to be picked up last monday. I made an appointment for wednesday night knowing very well that my boxes weren't even finished. How hard could it be for a cabinet maker to whip together two deep boxes, 15 frames with plastic foundation, a top feeder, an inner cover, a telescoping cover, and a screen bottom board in one night and then prime and paint it?
Well, I managed. I picked up my nuc on wednesday night. The bee keeper told me to immediately add a second deep and to feed them once. I took the nuc home and sat it on top of my shiny new hive and removed the foam from the nuc box entrance and watched as the first few bees ventured out. It was pretty cool to see. So I decided that they had been traumatized enough with their new surroundings and I was going to give them a day before i installed them in my new hive. So Friday, I got geared up. I sprayed all the frames in both boxes with a 1:1 syrup with Pro Health added in. I carefully installed the five frames in the same order in the bottom box. I quickly looked them over for a queen, but I'm about as observant as a 6 month old and didn't see her. I then added the other five frames and the second box. I gave them a gallon of 1:1 with pro health and closed everything up. Over the past few days I've observed the bees flying out and returning completely loaded with pollen. It's encouraging to see I assume. But yesterday while I was satisfying my obsession with the bees, I noticed that in my haste, I completely forgot to cut down the second deep box. So it's a full 11 1/4" deep. I've been wrestling with this in my mind, and am convinced that there is a reason that they are supposed to be 9 5/8" and that my queen won't go upstairs to lay.
My questions are how imperative is it to get that second one off and cut down? Is it something that I should do immediately? I'd say 3 1/2 frames of the nuc were capped, but I'm new, so I don't really know what the heck I was looking at. I think the earliest I'll be able to get to it will be saturday. Is that soon enough? Am I wrong about the queen not going up? Also, I've noticed that the workers really seem to like hanging out in my hand holes that are cut into the boxes. Is that normal? Any help would be greatly appreciated.