Just like software engineers, the longer you keep bees, the more things you do without thinking about it. It can be hard for established engineers and beekeepers alike to remember all the things that they had to find or figure out on their own, and so some topics just don't come up in books.
After four years of beekeeping, I feel like I'm on the edge of beginning to forget what being a newbie was like, and forgetting all the questions I had. Luckily, I kept a lot of notes!
It's said that if you ask ten beekeepers a question, you'll get a dozen different answers. These are my answers to things, so you'll have to come up with another three or four answers to really round it out.
The inner cover was the most mystifying piece of equipment when I first started. I have two basic models. One is flush and flat on one side with a rim on the other, and a notch for an entrance. The other has a shallow rim on one side, and a deeper rim on the other, with the notch.
Most of the time, I want the smallest gap down. So small rim, or flat side towards the bottom of the box. That way the space above the bars is bee space and they will not build too much burr comb in there.
The only time I flip the inner cover over is to add space for a pollen patty, or to add an upper entrance during a honey flow.
If you want the upper entrance, you'll need to slide your outer cover towards the notch, leaving a gap on that side. If you need the rim down for a patty, but do not want an upper entrance, slide the outer cover back to block it as best you can.
I'm personally moving towards migratory, single piece covers and using shims when I need space for a patty.
I've made honey using queen excluders, and I've made honey without them. I have not noticed a difference, so I now default to using them to keep my honey comb clean and brood free. I'm sure over time I will go without them again some times, as cleaning them is an annoying task and I'm bound to be ready to super and have no usable excluders.
I've only ever used the plastic ones, and put the horizontal ridges towards the bottom of the hive, if it is not flush on both sides. Those ridges maintain bee space between the tops of the bars on the lower box and the excluder, making it so the bees are less inclined to glue the whole exlcuder down with propolis.
You should also remember that this is not just useful for making honey. A queen excluder is an invaluable tool for manipulating a queen.
For example, if you need to find her but you can't, put an excluder between the boxes. Come back in three or four days and check the top box first, then the bottom. Wherever the eggs are is the box the queen is in, since anything laid before you put on the excluder should have hatched by now. That easily rules out 10 frames for you to look through. You can use this to make splits, as after three more days the top box is hopelessly queenless and has no way to raise their own. Pull the frames you want, dump in the bees you need, and add a queen cell or mated queen.
If you're in a rush, you can do basically the same thing to isolate the queen by (gently) shaking all the bees into the bottom box, putting on the excluder, and coming back later or the next day. The workers should have moved up and equalized between the boxes (more or less) but the queen will be down in the bottom box, so you can eliminate searching half of your frames that way.
Drone trapping is done by using special frames which are sized for drone comb, rather than worker cells. The idea is that varroa prefer the larger cells, and more go into the drone comb. You then take the frames out when they are capped and kill the larvae and the mites with them. If you've ever seen bright green plastic frames, that is drone frames.
This is a pretty easy win if you can get into your colonies regularly, but you don't want to miss your timing or you're helping the varroa instead of hindering them. You've got about two weeks from the first capped drones to emergence, so don't miss it.
I'm leaning towards no longer using these frames, even though my chickens and ducks love cleaning them out, as I'm very bad at remembering to deal with them.
Have A Goal
Whenever you go into a hive, have a specific goal (or goals) in mind. When you accomplish that goal, get out. Seriously, be done when you get there, unless you see something concerning. The more you mess with a colony, the more effort it takes them to recover from your inspection. My most common goals are:
Is this colony queenright?
Once you see eggs or young larvae, you're done. You almost never have to actually find her, you just have to prove she was there recently.
Is this colony preparing to swarm?
Tilt the brood chambers up and look for cells. Yes, they will build them higher up on the frame, but they will almost always build some at the bottom. You're pretty safe to just check the bottom, and you never even have to lift a frame.
Does this colony have enough food?
When they are raising bees, you have to pull at least one or two brood frames, but that is all. Look for a band of pollen and then move on. In the late fall or winter, just lift the box and see how heavy it is. Honey is the main need in winter, so it's all about weight. It does take time to learn what a deep with 60lbs of honey feels like vs 30lbs, but heavy is heavy and that's a good start. I have rarely regretted feeding. If they don't need it, they just won't take it.
Does this colony have enough space?
Pull some frames in the brood nest. If they are a patchy mix of brood and nectar, they're honey bound. It should only take a frame or two to tell.
The one exception to this is when you get started keeping bees. I think you should really poke around that first year, see what the colony looks like during each phase of the year, from top to bottom. Yes, you will be setting them back, but they will recover, and you're not trying to make honey on year one anyway. This helps you get comfortable with the bees and with manipulating a colony, which is a requirement for keeping bees well.
Take the level of notes that works for you, but make sure you take notes.
My first year I would take a hive all the way apart, and note down how much brood, honey, pollen, frame by frame. Looking back that feels absurd, but at the time it told me a lot about my bees. I also only had one colony (I should have had two). Some people write notes on their outer covers, some people leave cryptic messages with the position of the bricks on top of their hives. I keep succinct notes on my phone, and a todo list for anything that I need to do next time, or at a certain date.
Do what feels right for you. But the worst thing you can do is not take notes. You will forget something and cause yourself and your bees a problem. And wouldn't it be nice to look back on your notes and have hints as to why your colony is in the state it is in?
Bees can be a lot of fun. Don't overthink it, try things out to see what works for you, and keep an eye on your mite counts.