I didn't read the responses, so if this has already been said, I apologize...
First, I make a color copy of the pattern so I can write on it.
Second, if I have swapped out colors, I neatly line through the color called for in the pattern, and write my color choice right next to or above the original. It helps me to keep focused on what I am doing to have my colors labeled according to what I am using.
Have you ever tired a Thimbleberries pattern? The directions are crystal clear, in my opinion. Each step for each block is written in great detail. As you build a block, or join blocks, they always tell you how big your block should be. It really helps to keep things straight and even. You can often score used Thimbleberries patterns on ebay. Sorry, none of mine are for sale!!