So after a bit, your campaign is going to have lots of notes, side adventures and plots and character info. Here's my suggestion. Have a two inch (or bigger) binder with all the following in it so you have easy access to everything you need to know:
1) A running plot. I have a spiral (though loose paper works, as well) where I right down my running plot. Not necessarily the nuts and bolts (though that's in there as well), but the main idea. So my characters in my current campaign are looking for a series of artifacts. I have written down where they are, the order their patron will send them to get them and notes as to what they have found so far. I also have a list of sub plots (like introducing followers) just so I know what I need to throw in at some point.
2) Characters. I like to have copies of the character sheets where I can look at them and plan something special for that character or try to get them to use a skill they have put points in but never get to use. Plus, I don't really want to throw creatures at them that they have nothing they can use to stop them.
3) NPCs and major bad guys. Got to have the people and villains they are interacting with somewhere. This way they are all together and you don't have to scramble to make a new one because you lost the old one.
4) Treasure lists. Character sheets get lost, it happens. And your copy may not be up to date. So this way you can always go back and tell your player, yes, you had this item. But this also holds true that the character may not have had said item.
5) Maps and graphing paper. Players like to know where they are going and where they have been. So having old maps as well as graphing paper to lay out new ones is always a good thing.
6) List of random names. For those NPC's that just pop up during the game.
7) Extra character sheets. For those times your players just can't manage to stay alive.