It's all in the storytelling. Having editors helps with that. But what I've noticed in Brandon's books (and also in Terry Pratchett's books) is that little things are there for a reason. It's that attention to the details that makes a difference. Small things in the beginning that the reader ignores but by the end are found to be important details.
I think that's key. The question is--how do you know which little things should matter in the end? I think you need a very clear vision of how the story will end. Not just in general, but very clearly, very specifically. Maybe that vision doesn't come until you've actually written it. If that's the case, you'll have to go back and retro-fit the ending, filling in gaps and making changes where necessary. Along the way, you may even think of more things to add to the ending, and then have to change the ending to fit it. If you have that vision from the start, you can do all that from the start, but even then, I imagine things will occur during the book that you didn't foresee, and you'll have to change the ending.
Here are some examples.
By the time the ending comes around, I was relatively convinced that Sazed's bracers were pretty unimportant in how the ending would happen. They were still important to his personal conflict, but not to the resolution of the world conflict. Like him, I'd given up on them and accepted the fact that it was time to move on and accept some things on faith alone. Wasted effort. Noble, but wasted. And then--whamo! They become critical to the world conflict. It was a brilliant move on Brandon's part.
Same with Vin's earring. I' told my wife from the beginning that the earring was imporant. When Vin shot it through Marsh's head, I was pretty certain it's duty had been fulfilled. But then Brandon turns it around on us.
I don't think you can do that type of thing unless you know very clearly how the ending will happen. And I almost mean every little sentence, every tiny detail. The problem is that every little sentence, and every little detail, is a product of everything that came before it. For me, it almost becomes a chicken and egg question. I'd be curious to know how early in his writing process Brandon realized that the earring was a spike. Clearly before the end of Final Empire. How soon in his writing process did he know that the bracers would be so important?
It almost gets back to this, for me: world and character building. Make an interesting world and characters, and then figure out how you can do unexpected, interesting things in that world, with those characters.
Every paragraph I type leads me to a new topic, so I'd better stop, now.