I use Elenore Burns method of sewing and cutting. You do have to be careful you don't stretch the fabric as you're sewing or you will end up with different size squares. If you cut the strip and then sew this stretching is eliminated since you are making the strip fit the square. Each method has it's advantages.
I made a complex log cabin as far as color and size of logs were concerned and I drew a master and numbered the logs. I kept that in front of me for reference when I was putting my squares together. It sure made a difference in my sanity. I could also leave in the middle and come back and not have to wonder where I was because I could count the rows and match my master. Make a master with each piece numbered and then number your color strips. That should ease things.