I second the template idea, saves a lot of time instead of marking on each piece of fabric. Totally agree with using the freezer paper. In fact, you can leave the fabric the size of the freezer paper sheet and just draw the blocks on it without cutting them and cut them later.
Micron pens are great but expensive, especially if you want color ones. However, you can also buy permanent fabric markers in colors from craft stores that hold up extremely well to laundering for much less than the micron pigma pens. I have used Tulip fabric markers with good results after heat setting and following the package directions.