Marking your joints so you can't reassemble it wrong
Okay. Everything fits now. You clamped it up last time, you fixed the piece that needed fixing, and what you've got sitting on your bench right now is a shelf that goes together right. That's the good news.
The bad news, if you want to call it that, is that you're about to take it apart again. And once it's in a pile of separate boards, there is nothing stopping you from putting it back together wrong. Nothing at all. The wood doesn't remember which way it goes. You have to tell it, and the way you tell it is with marks.
I learned this one the hard way.
Years ago I glued a joint upside down. I don't mean slightly off, I mean the whole piece was flipped from how it needed to go. I didn't catch it going in, because in the moment everything sort of looks like it fits if you're not paying close attention, and I was excited to get glue on wood after doing all the careful work to get there. It wasn't until the next morning, clamps off, that I looked at it and thought, that's backwards. By then it was glued. Not great, but it held, actually, it held fine, it was just wrong, and I had to decide whether to live with it or take it apart and start over. I took it apart. Wasn't fun.
So now I dry fit every single joint before glue touches anything, and I mark every joint before I take the dry fit apart. Every time. No exceptions, doesn't matter how simple the project is. I recommend this to everyone I teach, because the five minutes it takes you now will save you from redoing a glue-up later, and glue-ups are a lot harder to undo than a clamp.
What you're actually doing
You're labeling each joint so that when you pick pieces back up off the bench, there is exactly one way they go together, and it's obvious.
Here's how I do it.
Pick a marking system and keep it stupid simple. I use letters. Side A gets an "A" near the top of every joint it touches. Side B gets a "B." If a shelf has a top and bottom and two sides, I might go A, B, C, D around the piece so I know not just which board but which one goes where.
Mark right on the joint, close to the edge that meets. Not out in the middle of the board where it won't help you. You want the mark right at the spot where two pieces come together, so when you're staring at a joint later trying to remember which way it goes, the answer is right there.
Use a pencil, not a pen, and use one you can find again. Pen bleeds into softwood a little and it's a pain to sand off later. A carpenter's pencil or a regular number 2 works fine. I keep mine in my apron pocket so I'm not hunting for it every five minutes, which, I feel like, is half of why people skip this step. They set the pencil down somewhere and by the time they find it again they've lost track of what they were marking.
Add an arrow if the orientation matters. If a board has a top and bottom that look nearly identical, and it will matter which way is up, draw a little arrow pointing "up" or "out" on the good face. This is exactly the mistake I made with that upside-down joint. It looked like it could go either way, and it couldn't.
Mark both sides of every joint, not just one. If you only mark board A, you still have to guess which unmarked board it goes with. Mark both, so the pairing is obvious even if the boards get separated and shuffled around on the bench, which they will, because that's what benches do to your pieces the second you look away.
Number the joints if you've got more than a couple. Joint 1, joint 2, joint 3. This matters more on bigger projects than this shelf, but it's a good habit to build now while the stakes are low.
A word on why this matters more than it looks like it should
Nobody wants to slow down for this step. You've got your dry fit sitting there, it looks good, you're ready for glue. I get it. But the whole reason we did the dry fit in the first place was to catch mistakes before they're permanent, and marking your joints is what carries that work forward. Otherwise you did all that checking for nothing, because you'll take it apart, set the pieces down, get distracted by something, and twenty minutes later you're guessing again.
Take the dry fit apart now, piece by piece, marking as you go. Don't rush it. This is a five-minute job that saves you from an hour of frustration, or from gluing a shelf together backwards and living with it, which I've done, and which I don't recommend.
Before next time: get your marked pieces stacked in order on the bench, in the sequence you'll pick them back up. Next lesson we talk about glue, and you'll want to grab pieces in the right order without stopping to think about it.