Chad,
Minn has it correct. Here are a couple of things I do that helps me. With the instructions and plans in front of you take the sheets with the parts on them (one at a time) and label every piece, write the part number directly on the piece. I then label all the flat and stick wood. Almost all kit instructions will have a list of all the sticks and flat pieces and their sizes. Use a ruler to identify each piece, right the size on the piece, and check it off in the instructions. This does 2 things, let's you inventory all of the wood to make sure the kit is complete (mistakes to occasionally happen) and it labels the pieces so you pick the correct piece while you are building. Pay particular attention to the stick lengths. It's common to have several different lengths of the same size stock (i.e. 1/8"x1/8"x24" and 1/8"x1/8"x36"). If you use the wrong piece in the wrong place you're going to have to make a trip to the LHS to complete replace the piece you used.

Hope this helps