It's not the greatest organizational system of all time, but sorting the Legos by shape, with crude categories like "1x3+" and all "sloped bricks" has saved me a ton of effort. Substituting alternate colors is the rule, rather than the exception when building things from books or online instructions. Back when we sorted by color, we'd always look for the brick in the specified color and wouldn't find it. Then, we'd try to find it in another color. There were cases in which we'd look through every box for a piece.
Now, the guy counts out the studs on the piece specified in the instructions, tells me what shape he needs, I point him to the box with that shape, and he usually finds it on his own.