CAD software is your friend. Also, unless you are buying your lumber from a mill which offers full dimensional stock, the materials aren't really the size they are labeled as.
I modeled a "saltbox" style 12x12 garage for my motorcycle and ATV completely in 3D CAD, before ever cutting a piece of wood. Of course, as soon as I had something fully designed, one of my buddies offered me a free garage door which I had to redesign for. The CAD software made this much easier as well. I then made a list of all of the pieces, and cut all of them before assembling a single part. It went together like a kit, with the exception of a couple of small things which were simple to fix. It's been up through two winters, with heavy sustained snow loads, and still looks like the day it was built.
Unless you are an experienced builder, there will always be something you forget to take into account. But seeing an exact scale, virtual representation, before you start cutting, can minimize the expensive gotchas.