Marking your joints so you can't reassemble it wrong
Everything goes together right now. You clamped it up last session, you sorted out the piece that needed sorting, and what's sitting on your bench is a shelf that fits. That's the good news.
The less good news, if you want to call it that, is that you're about to take the whole thing apart again. And once it's a pile of loose boards, nothing stops you from putting it back together wrong. Nothing. 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. Not slightly off, I mean the whole piece 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 so eager to get glue on wood after all the careful work leading up to it. It wasn't until the next morning, clamps off, that I looked at it and thought, that's backwards. By then it was glued. It held fine, actually, 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 a thing, and I mark every joint before I break the dry fit down. Every time. No exceptions, doesn't matter how simple the project is. I tell everyone I teach the same, because the five minutes it costs you now saves 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 the pieces back up off the bench, there's exactly one way they go together, and it's plain to see.
Here's how I go about 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 a bottom and two sides, I might run A, B, C, D around the piece so I know not just which board but which spot it lives in.
Mark right on the joint, close to the edge that meets. Not out in the middle of the board where it does you no good. You want the mark right where two pieces come together, so when you're staring at a joint later trying to remember which way it faces, the answer is sitting 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 plain number 2 works fine. I keep mine in my apron pocket so I'm not hunting it down every five minutes, which, near as I can tell, is half of why people skip this step. They set the pencil down somewhere and by the time they've found it they've lost the thread of what they were marking.
Add an arrow if the orientation matters. If a board has a top and bottom that look nearly the same, and it'll 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. Mark only board A and you're still guessing which unmarked board it pairs with. Mark both, so the pairing stays obvious even after 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 on 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. Your dry fit is sitting there, it looks good, you're ready for glue. I understand. But the whole reason we did the dry fit was to catch mistakes before they turn 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 pulled away by something, and twenty minutes later you're guessing all over again.
Take the dry fit apart now, piece by piece, marking as you go. Don't hurry it. This is a five-minute job that spares you an hour of frustration, or a shelf glued together backwards that you live with for good, which I've done, and 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 glue, and you'll want to grab pieces in the right order without stopping to think.